6MYQ

Avian mitochondrial complex II with ferulenol bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic studies of the binding of ligands to the ubiquinone site of mitochondrial respiratory Complex II

Huang, L.-S.Berry, E.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase cytochrome b, large subunit
C
140Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Find proteins for D0VWW3 (Gallus gallus)
Go to UniProtKB:  D0VWW3

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial
D
103Gallus gallusMutation(s): 0 
Gene Names: SDHDRCJMB04_23p7
Find proteins for Q5ZIS0 (Gallus gallus)
Go to UniProtKB:  Q5ZIS0

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
A
621Gallus gallusMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Find proteins for F1NPJ4 (Gallus gallus)
Go to UniProtKB:  F1NPJ4

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
B
252Gallus gallusMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Find proteins for Q9YHT2 (Gallus gallus)
Go to UniProtKB:  Q9YHT2
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
3PE
Query on 3PE

Download CCD File 
D
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
 Ligand Interaction
HEM
Query on HEM

Download CCD File 
C
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
UMQ
Query on UMQ

Download CCD File 
C
UNDECYL-MALTOSIDE
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
 Ligand Interaction
9AU
Query on 9AU

Download CCD File 
C
4-oxidanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one
C24 H30 O3
NJJDBBUWWOAOLD-CFBAGHHKSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
B
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download CCD File 
B
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FES
Query on FES

Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

Download CCD File 
A
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download CCD File 
A, B, C, D
Unknown ligand
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
C
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.91α = 90
b = 84.553β = 90
c = 290.523γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United States1R01GM062563

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence