MolNFT v1 · #137234 · protein

Crystal structure of anti-zika antibody Z004 bound to denv-1 envelope protein diii

5VIC · Fab heavy chain: “Crystal structure of anti-zika antibody Z004 bound to denv-1 envelope protein diii”. X-ray diffraction, 4 pockets (best druggability 0.56). MolNFT v1 #137234 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5VIC
Type: protein
Length: 513 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain; Dengue 1 envelope diii domain
UniProt: S6B291, P0DOX7, P17763
Pockets: 4 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	219	7% helix, 48% strand	S6B291
L	Fab light chain	protein	211	5% helix, 49% strand	P0DOX7
E	Dengue 1 envelope diii domain	protein	83	4% helix, 49% strand	P17763

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	447	0.56	0.73	52	empty
2	74	0.33	0.75	15	empty
3	92	0.32	0.73	22	empty
4	76	0.31	0.74	18	empty

Interfaces

3 interfaces between chains.

H–L · 1788 Å² buried · 20 hydrogen bonds · protein-protein
H–E · 465 Å² buried · 8 hydrogen bonds · protein-protein
L–E · 445 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5VIC · Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII · the same entry in another collection · chain H against H, 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 0.97

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 P17763
Elsewhere: RCSB PDB 5VIC · PDBe 5VIC · UniProt S6B291 · UniProt P0DOX7 · UniProt P17763

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