MolNFT v1 · #137238 · protein

Crystal structure of anti-zika antibody Z006 bound to zika virus envelope protein diii

5VIG · Fab heavy chain: “Crystal structure of anti-zika antibody Z006 bound to zika virus envelope protein diii”. X-ray diffraction, 8 pockets (best druggability 0.68). MolNFT v1 #137238 on GenesisL1: 3D structure, binding sites and…

PDB: 5VIG
Type: protein
Length: 1,050 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Zika virus envelope protein diii
UniProt: S6B291, P0DOX7, A0A1I9ZK43
Pockets: 8 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Fab heavy chain	protein	213	8% helix, 48% strand	S6B291
L, B	Fab light chain	protein	212	6% helix, 50% strand	P0DOX7
Z, G	Zika virus envelope protein diii	protein	100	3% helix, 50% strand	A0A1I9ZK43

Ligands and binding sites

FLC · Citrate anion · additive · chains A

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	886	0.68	0.74	97	empty
2	401	0.56	0.74	47	empty
3	118	0.53	0.82	25	empty
4	156	0.53	0.79	28	empty
5	145	0.44	0.76	22	empty

Interfaces

7 interfaces between chains.

H–L · 1657 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1652 Å² buried · 13 hydrogen bonds · protein-protein
L–B · 761 Å² buried · 11 hydrogen bonds · protein-protein
A–G · 593 Å² buried · 11 hydrogen bonds · protein-protein
H–Z · 580 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5VIG · Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII · the same entry in another collection · chain Z against Z, TM-score 1.00
P0DOX7 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa light chain (P0DOX7) · a predicted model of the same protein · chain L against A, TM-score 0.84

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 A0A1I9ZK43
Elsewhere: RCSB PDB 5VIG · PDBe 5VIG · UniProt S6B291 · UniProt P0DOX7 · UniProt A0A1I9ZK43

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