MolNFT v1 · #122475 · protein

Crystal structure of 10E8V4 Fab in complex with an HIV-1 GP41 peptide.

5IQ9 · 10E8V4 heavy chain: “Crystal structure of 10E8V4 Fab in complex with an HIV-1 GP41 peptide.”. X-ray diffraction, 13 pockets (best druggability 0.62). MolNFT v1 #122475 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5IQ9
Type: protein
Length: 910 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 10E8V4 heavy chain; 10E8V4 light chain; GP41 mper peptide
UniProt: P01857, P0CG05, Q1HSF8
Pockets: 13 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H	10E8V4 heavy chain	protein	227	7% helix, 53% strand	P01857
B, L	10E8V4 light chain	protein	210	9% helix, 50% strand	P0CG05
C, P	GP41 mper peptide	protein	18	67% helix, 0% strand	Q1HSF8

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	413	0.62	0.77	62	empty
2	565	0.61	0.74	65	empty
3	67	0.55	0.88	19	empty
4	335	0.53	0.74	42	empty
5	244	0.52	0.76	33	empty

Interfaces

9 interfaces between chains.

H–L · 2214 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 2198 Å² buried · 22 hydrogen bonds · protein-protein
H–P · 711 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 693 Å² buried · 5 hydrogen bonds · protein-protein
B–L · 423 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5IQ9 · Crystal structure of 10E8v4 Fab in complex with an HIV-1 gp41 peptide. · 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
Every structure of UniProt P01857
Every structure of UniProt P0CG05
Every structure of UniProt Q1HSF8
Elsewhere: RCSB PDB 5IQ9 · PDBe 5IQ9 · UniProt P01857 · UniProt P0CG05 · UniProt Q1HSF8

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