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Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an nof V3 peptide

Analyse Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an nof V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MLV
Type: protein
Length: 905 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain; Human monoclonal…
UniProt: Q79790
Pockets: 13 · best druggability 0.71

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain	protein	218	6% helix, 51% strand	—
H, N	Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab heavy chain	protein	221	7% helix, 55% strand	—
P, Q	HIV-1 GP120 third variable region (V3) crown	protein	13	0% helix, 54% strand	Q79790
M	Human monoclonal anti-HIV-1 GP120 V3 antibody 2557 Fab light chain	protein	219	8% helix, 50% strand	—

Pockets

13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.71	0.78	95	empty
2	130	0.51	0.81	24	empty
3	124	0.48	0.79	23	empty
4	197	0.46	0.74	31	empty
5	78	0.40	0.78	13	empty

Interfaces

9 interfaces between chains.

M–N · 1954 Å² buried · 20 hydrogen bonds · protein-protein
L–H · 1897 Å² buried · 15 hydrogen bonds · protein-protein
H–P · 504 Å² buried · 10 hydrogen bonds · protein-protein
N–Q · 475 Å² buried · 7 hydrogen bonds · protein-protein
L–P · 381 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3MLV · Crystal structure of anti-HIV-1 V3 Fab 2557 in complex with an NOF V3 peptide · 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 Q79790
Elsewhere: RCSB PDB 3MLV · PDBe 3MLV · UniProt Q79790

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