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3D View User Guide

The 3D View option from the RCSB PDB structure summary page utilizes the WebGL-based NGL Viewer [Rose2015], [Rose2016], to display PDB structures in three-dimensions.

Various general display options are available from the main window and three types of views are available:

General Display Options

Various display options are available from the main section of the 3D view page:

Mouse Controls

Rotate the view around the center of the canvas Translate the view and move the center of rotation Zoom the view in and out Show information (tooltips) about the object close to the mouse cursor or finger tap such as atoms or bonds Move the clipping/focus planes in and out Increase/decrease the isolevel value of the selected electron density map Combination "Move the clipping/focus planes in and out" and "Zoom the view in and out" Distance, angle, dihedral measurements. Pick to select/deselect 1 to 4 atoms to start a measurement. Finish a measurement by picking an atom twice in a row. Depending on how many atoms are selected the distance (2 atoms), the angle (3 atoms) or the dihedral (4 atoms) is measured. Picking no atom deselects all atoms. To remove a measurement select all involved atoms and pick the last atom twice in a row.

Structure View

Various display options are available from the Structure View tab of the 3D view page:

Color schemes

N-terminus C-terminus
Rainbow - blue is the N-terminus and red is the C-terminus

First chain Last chain
By Chain - colored by chain as found in the asymmetric unit

High B-factor Low B-factor
By B-factor - colored from red (highest B-factors in the structure) to tan (lowest B-factor in the structure)

Hydrophilic Hydrophobic
By Hydrophobicity -- colored from red (hydrophilic) to green (hydrophobic). It uses the experimentally determined hydrophobicity scale based on whole residue free energies of transfer ΔG (kcal/mol) from water to POPC interface as reported by Wimley and White.

H
C
N
O
F
P
S
By Element/CPK

Ala
Arg
Asn
Asp
Cys
Gln
Glu
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Gln
Val
By Residue - Amino acids

A/DA
G/DG
I/DI
X/DX
C/DC
T/DT
U/DU
D/DD
By Residue - Nucleotides

alpha-helix
3/10 helix
pi helix
beta strand
beta turn
coil
DNA
RNA
carbohydrate
By Secondary Structure (as determined by DSSP) plus DNA, RNA and carbohydrate

Structure View: Symmetry

Protein Symmetry

Protein symmetry refers to point group or helical symmetry of identical subunits (>= 95% sequence identity over 90% of the length of two proteins). While a single protein chain with L-amino acids cannot be symmetric (point group C1), protein complexes with quaternary structure can have rotational and helical symmetry.

Complexes are considered symmetric if identical subunits superpose with their symmetry related copies within <= 7 Å Cα RMSD. Protein subunits are considered identical if their pairwise sequence identity is >= 95% over 90% of the length of both sequences, to account for minor sequence variations such as point mutations and truncated or disordered N- and C-terminal segments. Protein chains with less than 20 residues are excluded, unless at least half of the chains are shorter than 20 residues. Nucleic acids and carbohydrate chains, as well as ligands are excluded. Split entries (entries divided between multiple coordinate files due to the limitations of the PDB file format) are currently excluded from the protein stoichiometry and protein symmetry features.

Protein Pseudosymmetry

Pseudosymmetry refers to symmetry of homologous protein subunits. Protein complexes with pseudostoichiometry may have a higher structural symmetry than the symmetry calculated based on sequence identity. If we consider hemoglobin again, at a 95% sequence identity threshold the alpha and beta subunits are considered different, which correspond to an A2B2 stoichiometry and a C2 point group. At the structural similarity level, all four chains are considered homologous (~45% sequence identity) with an A4 pseudostoichiometry and D2 pseudosymmetry.

Global Symmetry

Global symmetry refers to the symmetry of the entire complex. Protein complexes may be symmetric, pseudosymmetric, or asymmetric.

Local Symmetry

Asymmetric protein complexes may have local symmetry. Similar to global symmetry, we distinguish local symmetry of identical subunits and local pseudosymmetry of homologous subunits.

Structure View: Color (By Density Fit and By Geometry Quality) and Clashes option

wwPDB Validation Reports are available for every entry in the archive to provide an assessment of the quality of a structure and highlight specific concerns by considering the model coordinates, experimental data, and fit between the two. RCSB PDB Structure Summary pages contain the "slider" graphic that provides a visual summary, and link to the full report (PDF).

The Color 'By Density Fit' and 'By Geometry Quality' options map wwPDB Validation Report information onto the 3D structure. Clashes can be displayed as pink disks using the "Clashes" toggle.


3D Validation report options

Color By Density Fit

For structures determined using X-ray crystallography for which structure factors have been deposited, the "Density Fit" scheme colors a structure according to the quality of agreement between the model and the experimental electron density. Blue indicates a good fit for a residue and red a bad fit. Residue coloring is determined using normalized Real Space R (RSRZ) for polymer residues and real space correlation coefficient (RSCC) for ligands. Colors range from red (RSRZ = -2 or RSCC = 0.678) - through white - to blue (RSRZ = 0 or RSCC = 1.0):

Better Poor
Key: Color by Density Fit

The images below have been colored using the "Density Fit" scheme. On the left is a structure of Endoglucanase A (PDB ID 3WY6) with a generally good fit; on the right a structure of Ribonuclease P protein component 3 (PDB ID 3WYZ), which has areas of more problematic fit. For details regarding RSRZ and RSCC, please consult the Validation Report User Guide for X-ray structures.


Hydrolases colored using the "Density Fit" scheme.

Color By Geometry Quality

The "Geometry Quality" coloring scheme colors each polymer residue and ligand molecule according to the number of geometric issues (blue for 0, yellow for 1, orange for 2, and red for 3 or more):

0
1
2
≥3
Key: Color by Geometry Quality, # of geometry problems

Protein residues and nucleotides are colored per residue whereas ligand molecules are colored per atom. Possible geometric issues include steric clashes, Ramachandran or RNA backbone outliers, and sidechain conformation outliers.

The image below shows PDB entry 1FCC, a 3.2 Angstrom resolution structure with worse overall quality relative to all X-ray structures colored by Geometry Quality.


PDB entry 1FCC, a 3.2 Angstrom resolution structure with worse overall quality relative to all X-ray structures colored by Geometry Quality.

Clashes option

With this option, clashes between pairs of atoms are displayed as pink discs, with the size of each disc reflecting the degree of van der Waals (vdW) overlap between the two atoms. Clash display is currently not available for structures comprising more than 10,000 residues. Information on how these geometry quality criteria are calculated is available at wwPDB.org.

In the image below a clash between two atoms in entry 1D66 is indicated by a pink disc, showing how much the atoms' vdW spheres overlap. In this example, the structure has been colored using the "Geometry Quality" scheme, which indicates that this clash is the only geometric issue for these two residues.


A clash between two atoms in PDB ID 1D66 is indicated by a pink disc, showing how much the atoms' vdW spheres overlap. In this example, the structure has been colored using the "Geometry Quality" scheme, which indicates that this clash is the only geometric issue for these two residues.

Ligand Viewer Options

For entries containing ligands, the Ligand View offers various ligand-related display options:


hydrogen bonds

hydrophobic contacts

halogen bonds

metal interactions

cation-pi interactions

pi-stacking interactions

Note that there might be no binding pocket surface because the ligand is not interacting/not close enough with/to the macromolecule. The binding pocket surface is a surface of the macro molecule, that is, it ignores ligands, water, ions, ...

Interaction Types Definition and Calculation Parameters

Hydrogen Bonds

Hydrogen bonds [Stickle1992], [Zhou2008] are calculated according to the following parameters between donor and acceptor atoms.

Note that hydrogens are not required for the generation of hydrogen bonds, and indeed are ignored if present. While the aim is to find all potential hydrogen bonds a comprehensive global analysis to find the optimal hydrogen bonding network is not performed as this would require a global analysis of protonation states.

Donor atoms: In general all nitrogen, oxygen, and sulfur atoms that have a hydrogen count greater 1 according to our valence model can be considered donors (for carbon as a donor see the heading Weak Hydrogen Bonds). Any nitrogen in a His ring may also be a donor.

Acceptor atoms: All oxygen atoms are considered to be acceptors. Nitrogen atoms are considered to be acceptors when the charge is less than 1 and at least one lone pair is not conjugated according to our valence model. Aminoacids (table-based, in addition to the general rule). Any nitrogen atom in a ring in His (to work around the ambiguity of where the charge is). Sulfur atoms are considered to be acceptors if the formal charge is -1 or if they are present in Cys or Met.

The maximum donor to acceptor distance is generally 3.5 Å and 4.1 Å for bonding with sulfur atoms. Angles are checked according to the following guidelines:


Legend: Donor (D), Hydrogen (H), Donor-Antecedent (DA), Donor-Antecedent-Antecedent (DAA), Acceptor (A), Acceptor-Antecedent (AA), Acceptor-Antecedent-Antecedent (AAA).

Halogen Bonds

Halogen bonds [Auffinger2004] are calculated according to the following parameters: Donors can be X-C, where X is Cl, Br, I or At but not F (no sigma-hole). Acceptors can be Y-{O|N|S} where Y is C, P, N, or S. The maximum Halogen bond distance is 3.5 Å. The maximum angle deviation is 30 degrees optimal in which the C-X···O angle ≈180° (consistent with a strong directional polarization of the halogen) and the X···O-Y angle ≈120°.

Hydrophobic Contacts

Hydrophobic contacts [Freitas2017] are calculated according to the following parameters: Contacts are made between carbons that are connected only to carbon or hydrogen, the default maximum hydrophobic distance is 4.0 Å, for atoms that interact with several atoms in the same residue, only the one with the closest distance is kept, and hydrophobic contacts between pi-stacked aromatic rings are removed.

Metal Interactions

Metal Interaction types are defined as dative bonds and ionic/ionic-type interactions between metal classes and potential metal binding partners.

Potential metal binding partners
Nucleobases Aminoacids Halogens Functional groups from ligands
Metals classes
Alkali & Alkaline earth Li, Na, K, Rb, Cs, Mg, Ca, Sr, Ba and other Al,Ga,In,Tl, Sc, Sn, Pb, Bi, Sb, Hg Transition metals Actinides & Lanthanides & Y

Pi Interactions

Cation-Pi

Cation-Pi interactions [Gallivan1999] are defined as a contact between a positive charge center (see heading "Charge centers" below) and aromatic ring (see heading "Pi-Stacking" below) in wihch the maximum distance between ring and charge center is 6 Å and the maximum offset of ring and charge center is 1.5 Å.

Pi-stacking

Pi-stacking interactions [McGaughey1998] are the parallel or T-shaped stacking of aromatic rings. The aromaticity of a ring is deduced from flags of its member atoms (when available) or by checking if the ring is planar and contains only B, C, N, O, Si, P, S, Ge, As, Sn, Sb, Bi atoms. These interactions are included when the maximum distance between ring centers is 5.5 Å. The maximum offset of ring centers is 2.0 Å (about the radius of benzene plus 0.5 Å), the maximum deviation from optimal angle (0 for parallel, 90 for t-shaped) is 30 degree.

Charge centers

Positive charge centers can be: nitrogen sidechain atoms in Arg, His, Lys; atoms in Guanidine, Acetamidine groups; atoms with a positive charge according to our valence model. Negative charge centers can be: oxygen sidechain atoms in Glu, Asp; atoms in Sulfonic Acid, Phosphate (including DNA/RNA), Sulfate or Carboxylate; atoms with a negative charge according to our valence. Hydrogen bonds between atoms in the charge groups are not shown.

Electron Density Maps

Electron density maps combine the structural model (coordinates) and the experimentally-collected data from an X-ray structure determination and serve to represent the fit of the model to the data. There are two types of electron density maps commonly used by researchers: the 2fo-fc map and the fo-fc map. The fo-fc (also called a difference or omit map) map shows what has been overrepresented or not accounted for by the model, while the 2fo-fc map includes the fo-fc map and electron density around the model.

These two maps are then used to correct the model when possible. Even in the best quality structures, there are areas of poor electron density, which may represent sections of the model that exist in multiple conformations. This can be seen in long side chains or surface loops of the model.

For additional background, please see Structure Factors and Electron Density at PDB-101 and for additional information on the generation and downloading of maps at the RCSB, please see the X-ray Electron Density Maps FAQ.

The Electron Density Maps tab offers various display options:

References