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Crystal structure of the cluster II Fab 1281 in complex with HIV-1 GP41 ectodomain

Analyse Crystal structure of the cluster II Fab 1281 in complex with HIV-1 GP41… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3P30
Type: protein
Length: 521 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 GP41; 1281 Fab light chain; 1281 Fab heavy chain
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 GP41	protein	84	95% helix, 0% strand	—
L	1281 Fab light chain	protein	211	3% helix, 47% strand	—
H	1281 Fab heavy chain	protein	226	4% helix, 51% strand	—

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	442	0.57	0.74	52	empty
2	82	0.40	0.78	17	empty
3	115	0.39	0.75	27	empty
4	80	0.32	0.74	19	empty

Interfaces

3 interfaces between chains.

L–H · 1836 Å² buried · 12 hydrogen bonds · protein-protein
A–H · 485 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 308 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

3P30 · crystal structure of the cluster II Fab 1281 in complex with HIV-1 gp41 ectodomain · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 3P30 · PDBe 3P30

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