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Fab structure of anti-HIV-1 GP120 V2 mab 697

Analyse Fab structure of anti-HIV-1 GP120 V2 mab 697 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D9L
Type: protein
Length: 1,739 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Light chain of Fab fragment of anti-HIV1 GP120 V2 mab 697; Heavy chain of Fab fragment of…
UniProt: Q6GMX4, Q6GMX6
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Light chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	214	7% helix, 51% strand	Q6GMX4
H	Heavy chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	222	8% helix, 51% strand	Q6GMX6
M, N, O	Light chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	215	6% helix, 52% strand	Q6GMX4
I	Heavy chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	218	6% helix, 51% strand	Q6GMX6
J	Heavy chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	223	8% helix, 51% strand	Q6GMX6
K	Heavy chain of Fab fragment of anti-HIV1 GP120 V2 mab 697	protein	217	7% helix, 51% strand	Q6GMX6

Pockets

20 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.76	0.79	122	empty
2	556	0.65	0.77	77	empty
3	405	0.56	0.74	48	empty
4	93	0.49	0.82	19	empty
5	104	0.48	0.80	20	empty

Interfaces

11 interfaces between chains.

N–J · 1832 Å² buried · 16 hydrogen bonds · protein-protein
L–H · 1711 Å² buried · 16 hydrogen bonds · protein-protein
O–K · 1698 Å² buried · 16 hydrogen bonds · protein-protein
M–I · 1650 Å² buried · 16 hydrogen bonds · protein-protein
I–N · 565 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

4D9L · Fab structure of anti-HIV-1 gp120 V2 mAb 697 · the same entry in another collection · chain L against L, TM-score 1.00

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 Q6GMX4
Every structure of UniProt Q6GMX6
Elsewhere: RCSB PDB 4D9L · PDBe 4D9L · UniProt Q6GMX4 · UniProt Q6GMX6

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