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Crystal structure of Z032 Fab in complex with WNV EDIII

Analyse Crystal structure of Z032 Fab in complex with WNV EDIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UTE
Type: protein
Length: 2,269 residues
Chains: 11
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.9
Source: Homo sapiens; West Nile virus
Molecule: Z032 Fab heavy chain; Z032 Fab light chain; Envelope domain III
UniProt: S6B291, P0DOX7, Q06C97
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.9 · 7 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Z032 Fab heavy chain	protein	219	11% helix, 52% strand	S6B291
D, B, F, J	Z032 Fab light chain	protein	213	6% helix, 54% strand	P0DOX7
S	Envelope domain III	protein	98	0% helix, 46% strand	Q06C97
A, G	Z032 Fab heavy chain	protein	223	4% helix, 51% strand	S6B291
E	Z032 Fab heavy chain	protein	220	7% helix, 48% strand	S6B291
H	Z032 Fab light chain	protein	210	6% helix, 46% strand	P0DOX7
I	Z032 Fab heavy chain	protein	224	5% helix, 50% strand	S6B291

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains C, D, B, E, F, I, J

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	762	0.77	0.82	89	empty
2	740	0.73	0.79	49	empty
3	685	0.70	0.78	68	empty
4	364	0.63	0.78	30	empty
5	409	0.62	0.77	56	empty

Interfaces

23 interfaces between chains.

I–J · 2004 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1977 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1911 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 1845 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1820 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide (disulfide).

Compared structures

6UTE · Crystal structure of Z032 Fab in complex with wnv ediii · the same entry in another collection · chain S against S, TM-score 1.00
P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain D against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt S6B291
Every structure of UniProt P0DOX7
Every structure of UniProt Q06C97
Elsewhere: RCSB PDB 6UTE · PDBe 6UTE · UniProt S6B291 · UniProt P0DOX7 · UniProt Q06C97

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