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Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with an mn V3 peptide

Analyse Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with an mn V3 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3MLX
Type: protein
Length: 906 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab light chain; Human monoclonal…
UniProt: P05877
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab light chain	protein	211	6% helix, 51% strand	—
H, I	Human monoclonal anti-HIV-1 GP120 V3 antibody 3074 Fab heavy chain	protein	228	5% helix, 53% strand	—
P, Q	HIV-1 GP120 third variable region (V3) crown	protein	14	0% helix, 21% strand	P05877

Pockets

5 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	1102	0.77	0.80	106	empty
2	1098	0.76	0.79	108	empty
3	196	0.48	0.75	37	empty
4	114	0.39	0.75	28	empty
5	69	0.34	0.76	16	empty

Interfaces

11 interfaces between chains.

M–I · 1799 Å² buried · 18 hydrogen bonds · protein-protein
L–H · 1755 Å² buried · 18 hydrogen bonds · protein-protein
H–I · 830 Å² buried · 7 hydrogen bonds · protein-protein
H–P · 709 Å² buried · 14 hydrogen bonds · protein-protein
I–Q · 618 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3MLX · Crystal structure of anti-HIV-1 V3 Fab 3074 in complex with an MN 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 P05877
Elsewhere: RCSB PDB 3MLX · PDBe 3MLX · UniProt P05877

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