5DK3

Crystal Structure of Pembrolizumab, a full length IgG4 antibody


Sequence Similarity Clusters for the Entities in PDB 5DK3

Entity #1 | Chains: A,F
Light Chain protein, length: 218 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 2 3 16616
95 % 2 3 17554
90 % 94 296 66
70 % 886 2682 2
50 % 2307 6927 1
40 % 2308 6928 1
30 % 2324 6975 1
Entity #2 | Chains: B,G
Heavy Chain protein, length: 444 (BLAST)
Sequence Similarity Cutoff Rank Chains in Cluster Cluster ID / Name
100 % 1 1 49389
95 % 1 1 44423
90 % 1 1 42542
70 % 3 10 4684
50 % 4 27 1454
40 % 4 33 1084
30 % 4 33 1144

Instructions

In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff.



View more detailed documentation on the redundancy reduction and sequence clustering procedure used by RCSB PDB.

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Rank PDB ID Entity ID Chains Description Details Taxonomy EC Number
1 6BJZ 2 L 5c8 Fab Light chain 9606
2 6O3D 1 L PGZL1 FAB LIGHT CHAIN 9606
3 4XCF 1 L 4E10 Fab light chain 9606
4 6O24 2 B 4498 Kappa light chain 9606
5 5X08 2 L Fab 4E10 Light chain 9606
6 6O3K 1 L PGZL1.H4K3 light chain 9606
7 4XAW 1 L 4E10 Fab light chain 9606
8 2VXV 2 L HUMAN IGG ABT-325 9606
9 4PTU 1 A Antibody pn132p2C05, light chain 9606
10 4XC3 1 L 4E10 Fab light chain 9606
11 4XC1 1 L 4E10 FAB LIGHT CHAIN 9606
12 6QCU 1 L Light chain 9606
13 6WIY 2 L Fab 54-1G05 light chain 9606
14 5CIN 2 L FAB 4E10 LIGHT CHAIN 9606
15 6CA7 1 L PCT64_13C light chain 9606
16 6MVL 3 L Antibody Fab fragment light chain 9606
17 3QQ9 1 C, L 101F LIGHT CHAIN 10090
18 5I1K 1 L FAB LIGHT CHAIN 9606
19 4JDV 2 B, L Fab light chain NIH45-46 Germ-line Light CHAIN, IG Kappa 9606
20 3QRG 1 L Fab light chain 9606
21 4XBE 1 L 4E10 FAB LIGHT CHAIN 9606
22 6WOS 2 L Fab AR3B light chain 9606
23 4HHA 1 A Fab KE5 Fab fragment KE5 9606
24 6DC4 2 L Fab AM22 Light Chain 9606
25 6VLN 2 L 4498 Fab light chain 9606
26 6UOE 2 L 3-25 Fab light chain 9606
27 6O26 2 B 3246 Fab light chain 9606
28 6WJ0 2 L Fab 54-4H03 light chain 9606
29 3EO0 1 A, C GC-1008 Fab Light Chain 10090
30 5CIL 2 L FAB 4E10 LIGHT CHAIN 9606
31 4PTT 1 A Antibody pn132p2C05, light chain 9606
32 4DGV 2 L HCV1 Light Chain 9606
33 6ULF 2 B 4498 Fab light chain 9606
34 6GFE 2 L, M Immunoglobulin gamma-4 light chain 9606
35 5IBU 1 B, L 6652 Light Chain 9606
36 4HH9 1 A, C Fab KE5, light chain KE5 Light chain 9606
37 4DGY 2 L HCV1 Light Chain 9606
38 2V7N 1 A, C, E, G IMMUNOGLOBULIN LIGHT CHAIN SYNTHETIC GENE, DERIVED FROM PHAGE DISPLAY OF THE HUMAN COMBINATORIAL ANTIBODY LIBRARY (HUCAL) FAB FRAGMENT, RESIDUES 1-255 32630
39 5TL5 1 L M2177 LIGHT CHAIN 10090
40 2FX7 1 L Fab 4E10 Light Chain 9606
41 5CSZ 2 B, L GANTENERUMAB FAB FRAGMENT LIGHT CHAIN FAB 9606
42 6QKD 2 L, M, O, T FAB LIGHT CHAIN 9844
43 6HKG 2 B FISW84 Fab Fragment Light Chain 9606
44 5DR5 2 L AbD09097 Fab light chain 9606
45 3FN0 1 L Fab Z13e1 light chain 9606
46 4MAU 1 L C2244 light chain SEE REMARK 999 10090
47 6GHG 2 B, L Fab light chain 9606
48 5I16 1 A, L FAB LIGHT CHAIN 9606
49 6O2C 2 B 4493 Kappa light chain 9606
50 6O3L 1 B, L PGZL1.H4K3 light chain 9606
51 4FQL 2 L monoclonal antibody CR8033 light chain Fab 9606
52 6O28 2 B, D 4493 Kappa light chain 9606
53 5GGQ 1 L nivolumab light chain 9606
54 5K9J 2 L 56.a.09 light chain 9606
55 5TF1 2 L O2-CC Fab Light Chain 9606
56 3TCL 2 B, L CH04 Light Chain Fab 9606
57 5E8E 1 A IGA FAB LIGHT CHAIN 9606
58 5GGS 2 B, D light chain 9606
59 6UYD 3 B, L Fab AR3C light chain 9606
60 2NXY 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
61 3SO3 2 B A11 FAB light chain 9606
62 6DKJ 2 B, L Fab light chain 9606
63 4WY7 2 L Fab 4E10Light chain 9606
64 6E56 3 I, J antibody H2214 light chain, K1642 9606
65 5FB8 1 A Anti-IL-16 antibody 14.1 Fab domain Kappa Chain 10090
66 4HIE 1 A Fab 023.102 9606
67 3QEG 2 L Fab fragment of human anti-HIV antibody N12-i2, light chain Fab light chain 9606
68 5Y11 2 B MAb 4-5 light chain 9606
69 2NY2 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
70 1RHH 1 A, C Fab X5, light chain 9606
71 4JPI 2 B, L Putative VRC01 germline Fab light chain 9606
72 6O2B 2 B, D, I, P 4493 Kappa light chain 9606
73 1IQD 1 A HUMAN MONOCLONAL BO2C11 FAB LIGHT CHAIN 9606
74 6DFJ 2 L anti-Zika antibody Z021, Light Chain 9606
75 2NY4 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
76 2NY3 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
77 6UYF 2 L Fab AR3B light chain 9606
78 5I1A 1 A, L CNTO388 LIGHT CHAIN 9606
79 2NY1 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
80 6MTP 1 B, L Antibody VRC42.04 Fab light chain 9606
81 3X3F 2 L Light chain of KMTR2 9606
82 2NXZ 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
83 4HIH 1 A, C Fab 023.102 9606
84 6O2A 2 B, D, I, P 4493 Kappa light chain 9606
85 6NMS 1 A, L Fab 136 anti-SIRP-alpha antibody Variable Light Chain 9606
86 6URH 3 L AR3X Light Chain 9606
87 5V7R 1 L CBTAU-7.1 Fab light chain 9606
88 1DN0 1 A, C IGM-KAPPA COLD AGGLUTININ (LIGHT CHAIN) FAB FRAGMENT 9606
89 6N7U 2 B BDBV223 antibody light chain Fab 9606
90 3GIZ 1 L Fab fragment of anti-CD20 antibody Ofatumumab, light chain 9606
91 5NBI 2 L Design of antibodies 32630
92 3Q1S 1 L Z13e1 Fab light chain 9606
93 6U6U 2 L BI00655130 Fab light chain 9606
94 5DK3 1 A, F Light Chain 9606
95 6WIO 2 B Fab Light chain 9606
96 2NY0 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
97 1YYM 2 L, Q antibody 17b light chain ANTIGEN-BINDING FRAGMENT, FAB 9606
98 4QXG 2 L Fab, light chain, IgG1 Fab, light chain 9606
99 6XC4 3 L, Y CC12.3 light chain 9606
100 2I5Y 2 L, Q Antibody 17B Light chain ANTIGEN-BINDING FRAGMENT, FAB 9606
101 2FX9 1 L, M Fab 4E10 Light Chain 9606
102 1TZG 1 L, M Fab 4E10 light chain 9606
103 3W9D 2 B, D Antibody Fab light chain 9606
104 6O41 1 A, C, L germline PGZL1_gVmDmJ light chain 9606
105 6EYN 1 A, C, L 8D6 Fab light chain 8D6 Fab light chain 9606
106 4HWE 2 L Fab light chain light chain 9606
107 5TZ2 2 L C47B222 Fab Light Chain 9606
108 3W9E 3 B Antibody Fab light chain 9606
109 5TFS 2 L 02-K Fab Light chain 9606
110 5WT9 2 L Light Chain of Nivolumab 9606
111 4HIJ 1 A, C Fab 023.102 light chain 9606
112 7JMO 3 L COVA2-04 light chain 9606
113 6FG1 2 D LIGHT CHAIN OF FAB NAA32 9606
114 3EYF 1 A, C 8f9 Fab 9606
115 5I1C 1 L FAB LIGHT CHAIN 9606
116 5WNA 2 D, L mAb 3D3 Fab light chain 9606
117 1RZ8 1 A, C Fab 17b light chain 9606
118 5KZP 2 I, J, K, L HCV1-C1 Antibody Fab Light Chain 9606
119 5I1H 1 L FAB LIGHT CHAIN 9606
120 2FX8 1 L, M, N, O Fab 4E10 Light Chain 9606
121 6DFI 2 L anti-Zika antibody Z021, Light Chain 9606
122 5I1J 1 L FAB LIGHT CHAIN 9606
123 5CIP 2 B, L FAB 4E10 LIGHT CHAIN 9606
124 6WO4 3 L Fab HC11 light chain 9606
125 1I7Z 1 A, C CHIMERA OF IG KAPPA CHAIN: HUMAN CONSTANT REGION AND MOUSE VARIABLE REGION THE CHIMERA CONSISTS OF RESIDUES 1-108 OF MOUSE PORTION AND 109-214 OF HUMAN PORTION OF IG KAPPA CHAIN. 10090
126 6O29 2 B, L 4493 Kappa light chain 9606
127 4JPK 2 L Putative VRC01 germline precursor Fab light chain 9606
128 5XAJ 2 B, L FabHM14c10 light chain 9606
129 3X3G 2 L Light chain of KMTR2 9606
130 5IBT 2 L UCA Light Chain 9606
131 6CA6 1 A, L PCT64_35S light chain 9606
132 5XRQ 2 B, L Fab H3v-47 light chain 9606
133 2I60 2 L, Q ANTIBODY 17B LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
134 4NGH 1 L FAB LIGHT CHAIN 9606
135 2NY5 3 L ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
136 6NMU 1 A, L Fab 115 anti-SIRP-alpha antibody Variable Light Chain 9606
137 5JO4 2 B D80 Fab Light Chain 9606
138 5X8M 3 C durvalumab light chain 9606
139 1RZJ 3 L ANTIBODY 17B, LIGHT CHAIN FAB 9606
140 4HII 1 A, C Fab 023.102 light chain 9606
141 4DN3 1 L CNTO888 LIGHT CHAIN 9606
142 5WNB 2 L, M mAb 3D3 Fab light chain 9606
143 1GC1 3 L ANTIBODY 17B MONOCLONAL ANTIBODY 17B BINDS TO A CD4-INDUCED SITE ON GP120 ANTIGEN-BINDING FRAGMENT, FAB 9606
144 1G9M 3 L ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
145 6MFT 2 B, L Light chain glVRC01 9606
146 4HWB 3 L Fab light chain 9606
147 6B0A 2 L 1269 antibody, light chain 9606
148 2NYY 2 C CR1 monoclonal antibody light chain 9606
149 2GCY 1 A huC25 fab fragment light chain 10090
150 5JQD 1 A, B D80 Fab Fragment Light Chain 9606
151 6JC2 2 L ipilimumab fab light chain 9606
152 6RP8 2 L, l Antibody Ipilimumab light chain 9606
153 4KXZ 3 I, L, M, P GC1008 Light Chain 9606
154 6VTW 2 L 101F Fab Light Chain 10090
155 6CMI 2 C m102.3 light chain 9606
156 3EYQ 1 C M2J5 Fab 9606
157 6WOR 2 L Fab HC1AM light chain 9606
158 4XBG 1 B, D, F, I, K, L 4E10 Fab light chain 9606
159 1YYL 2 L, Q antibody 17b light chain ANTIGEN-BINDING FRAGMENT, FAB 9606
160 6MTQ 1 L Antibody VRC42.N1 Fab light chain 9606
161 2NY6 3 C ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
162 2AGJ 1 L Yvo Fab, Light Chain 9606
163 6VGR 3 D, L SC-003 Fab Light Chain 9606
164 3EYO 1 A, C 8f9 Fab 9606
165 5BZD 1 A, C 5G8 HIV Antibody light chain 9606
166 3B2U 1 D, G, K, L, O, R, U, X IMC-11F8 Fab Light chain 9606
167 4DN4 1 L CNTO888 LIGHT CHAIN 9606
168 6MHR 2 B, E Urelumab Fab kappa chain 9606
169 5TLK 1 A, E M2177 LIGHT CHAIN 10090
170 1IT9 1 L HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN FAB FRAGMENT 10090
171 6MTO 1 L Antibody VRC42.01 Fab light chain 9606
172 7CHC 2 L IGK@ protein 9606
173 5WI9 2 E, L 39F7 Fab light chain 9606
174 6BKC 2 L Fab AR3B light chain 9606
175 6XE1 2 L CV30 Fab Kappa chain 9606
176 4XCN 1 B, D, F, I, K, L 4E10 Fab light chain 9606
177 6B3S 3 D, G, K, L Necitumumab Fab Light chain 9606
178 3SDY 4 L Antibody CR8020, Light Chain 9606
179 6OED 2 B, D, L CH55 Fab light chain 9606
180 4NP4 3 L, M bezlotoxumab light chain 9606
181 4XCE 1 B, D, L 4E10 Fab light chain 9606
182 6M58 3 D, L Light chain of the SL335 antibody Fab 9606
183 4MWF 2 B, L Fab AR3C light chain 9606
184 6N8D 2 B, E A1431 Fab light chain 9606
185 4PS4 1 L M1295 LIGHT CHAIN 9606
186 5GGT 3 L IGK@ protein 9606
187 6OL5 4 L iglb12 Light Chain 9606
188 7CH5 2 L BD-629 Fab L 9606
189 3HI1 2 A, L F105 Light Chain 9606
190 1RZK 3 L ANTIBODY 17B, LIGHT CHAIN FAB 9606
191 6CMG 2 B m102.3 light chain 9606
192 6U38 3 L Fab Light Chain 9606
193 1G9N 3 L ANTIBODY 17B, LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
194 1QLR 1 A, C IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ) FAB FRAGMENT 9606
195 6PPG 2 A, L Fab MCAF5352A light chain 9606
196 5XMH 2 C, L YES8c light chain 9606
197 6UYM 3 B, L Fab AR3C light chain 9606
198 6O3U 1 A, C, E, L PGZL1.H4K3 light chain 9606
199 5I1G 1 L FAB LIGHT CHAIN 9606
200 4XCC 1 L 4E10 Fab light chain 9606
201 5Y2L 4 J a group 2 HA binding antibody AF4H1K1 Fab light chain 9606
202 4NHC 1 L FAB LIGHT CHAIN 9606
203 6U36 3 L Fab Light Chain 9606
204 5GMQ 3 C MCA1 light chain 9606
205 6CA9 1 A, C PCT64_LMCA Fab light chain 9606
206 6O25 2 B, F, J 3945 Kappa light chain 9606
207 5TRU 1 L, l Ipilimumab Fab light chain 9606
208 6XC7 5 D CC12.3 light chain 9606
209 6P9H 3 D, L Human anti staphylococcus aureus antibody STAU-281 Fab light chain 9606
210 6BKB 3 L Fab AR3A light chain 9606
211 6O42 1 A, L PGZL1_gVmDmJ light chain 9606
212 4YPG 1 A, L Sifalimumab light chain 9606
213 6NMR 1 B, G, K, L Fab 119 anti-SIRP-alpha antibody Variable Light Chain 9606
214 6MEF 2 L antibody AR3C Light Chain 9606
215 6WIR 2 B Fab light chain 9606
216 4UTA 3 L, M BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8 LIGHT CHAIN FAB FRAGMENT 9606
217 4KVN 3 L Human IgG Light Chain 9606
218 4KUC 2 D, E mAb6c2 fab-Heavy chain 10090
219 5VQM 2 C, L PA41 FAB LIGHT CHAIN 9606
220 5DUM 2 L 65C6 Light Chain 9606
221 3KYM 1 A, C, E, G, I, K, M, O Light Chain Li33 IgG2 9606
222 4OQT 2 L Light Chain of Li81 Fab, kappa 3 9606
223 3KYK 2 L Light Chain Li33 IgG1 9606
224 5TGB 2 B, L 02-CB Fab Light Chain 9606
225 5JOF 2 B, D, F, L VRC03 gLV light chain 9606
226 6WS6 2 B, D, F S309 antigen-binding (Fab) fragment, light chain 9606
227 4YWG 1 L, M Light chain of anti-HIV-1 gp120 V1V2 antibody 830A 9606
228 1U6A 1 L F105 LIGHT CHAIN ANTIGEN-BINDING FRAGMENT, FAB 9606
229 4XBP 1 B, D, F, L 4E10 FAB LIGHT CHAIN 9606
230 5K9K 2 B, L 56.a.09 Light chain 9606
231 5BZW 1 A 2B3 HIV Antibody light chain EIVLTQSPGTLSLSPGERATLSCRASQSVSAKNLAWYQQKPGQTPRLLMYGVSLRNTGVP DRFSGSGSGTDFTLTISRLEPEDSAVYFCQQYGTSPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 9606
232 5W4L 6 C, E Antibody N12-i3 light chain 9606
233 5NB5 1 L, M design of antibodies 32630
234 6WJ1 4 I, K, L Fab 54-4H03 light chain 9606
235 6B9J 3 B, L Fab vv138 Light chain 9606
236 5I17 1 A, L FAB LIGHT CHAIN 9606
237 4R8W 4 L Light chain of neutralizing antibody CT149 9606
238 5TPN 3 L hRSV0 light chain 9606
239 1I9R 3 L, M, Y IMMUNOGLOBULIN L 9606
240 6OZ9 3 L EBOV-520 Fab light chain 9606
241 5JXE 2 C, F Pembrolizumab Fab light chain 9606
242 5W42 4 L Fab H3v-47 light chain 9606
243 4JM2 3 C 17b Light chain Fab 9606
244 5GGR 2 B, L light chain 9606
245 5IBL 4 D, L 6639 Light Chain 9606
246 6T3J 2 B, G IgG1-hDR5-01-Light Chain 9606
247 6O3J 1 B, L PGZL1 light chain 9606
248 4N90 3 E, G, I Fab light chain 9606
249 4UBD 4 D, H, L, P, T, X monoclonal antibody L chain 9606
250 5D1Q 4 D P5 Light Chain 9606
251 6W4M 2 L ANTI-HIV ANTIBODY N12-I2 FAB LIGHT CHAIN 9606
252 6DC5 3 C, F, I Fab AM22 light chain 9606
253 3EO1 1 A, D, G, J GC-1008 Fab Light Chain 10090
254 5FEH 1 A, C, E PCT64_26 Fab light chain 9606
255 5UG0 3 C 2897 light chain 9606
256 6WOQ 5 H, K Fab HC1AM light chain 9606
257 6P91 3 L Fab 18.5C Antibody light chain 9606
258 6N7J 2 B, L BDBV223 antibody light chain Fab 9606
259 6PYC 2 L KoH body Fab light chain 10090
260 5D1X 4 D P5 Light Chain 9606
261 6UYG 3 L Fab AR3A light chain 9606
262 5WKO 2 B, D, F, H, J, L Antibody 27F3 light chain 9606
263 5UMI 2 B, L PA50 Fab Light chain 9606
264 6BKD 3 L Fab AR3D light chain 9606
265 6APD 3 E, G, I AM22 Fab Light Chain,Uncharacterized protein 9606
266 2NZ9 2 C, E AR2 monoclonal antibody light chain 9606
267 5Y2M 4 J, L a group 2 HA binding antibody AF4H1K1 Fab light chain 9606
268 6EYO 3 L, M 8D6 Fab light chain 8D6 Fab light chain 9606
269 3F12 1 A, C M2J1 Fab 9606
270 3B2V 1 L IMC-11F8 FAB Light chain 9606
271 5IGX 3 L germline NIH45-46 light chain 9606
272 6O3G 1 B, D, F, L PGZL1 light chain 9606
273 5KAQ 3 G, L, R ANTIBODY 31.A.83 FAB LIGHT CHAIN 9606
274 5W1K 3 C, H, M, N CR1-10 Fab light chain 9606
275 4XCY 1 B, D, F, I, K, L 4E10 Fab light chain 9606
276 5TLJ 1 A, E M2177 LIGHT CHAIN 10090
277 5TLJ 3 C, G M2191 LIGHT CHAIN 10090
278 6OFI 3 L CH55 Fab light chain 9606
279 2B4C 3 L anti-HIV-1 gp120 immunoglobulin X5 light chain 9606
280 5ESZ 2 B, L CH04 Light Chain 9606
281 6B3M 4 D, J, N, P, U, W 70-1F02 Fab Light Chain 9606
282 4RQS 2 C 17b Fab Light Chain 9606
283 6WIZ 4 L Fab 54-1G05 light chain 9606
284 7CBP 4 E, S Fab light chain 9606
285 6Y92 2 D, L Ofatumumab Fab light chain 9606
286 6PCI 5 Q, R, S rEBOV-520 Fab light chain 9606
287 6QD7 1 L, P, Z Light chain 9606
288 6MZJ 2 C, L VRC01GL light chain germline VK3-11 with the mature CDRL3 of VRC01 9606
289 6MYY 2 C, F, L VRC01GL light chain germline VK3-11 with the mature CDR L3 of VRC01 9606
290 6HJP 4 H, J, L Light chain of FISW84 Fab Fragment 9606
291 6HJQ 4 H, J, L Light chain of FISW84 Fab 9606
292 6CM3 4 J, L, N 17b Fab light chain 9606
293 5VN3 1 L, N, O 17b Fab light chain 9606
294 5THR 4 J, K, L 17b Fab VL domain 9606
295 5A8H 3 C, I, O FAB OF BROADLY NEUTRALIZING ANTIBODY 17B 9606
296 5A7X 3 C, G, K FAB OF BROADLY NEUTRALIZING ANTIBODY 17B 9606