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Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 GP120 core

Analyse Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 GP120 core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TIH
Type: protein
Length: 1,304 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 clade C ZM109F.PB4 GP120
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 11% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	HIV-1 clade C ZM109F.PB4 GP120	protein	326	11% helix, 33% strand	—

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	82	0.72	0.95	21	empty
2	75	0.70	0.94	19	empty
3	70	0.69	0.95	21	empty
4	284	0.69	0.84	46	empty
5	72	0.69	0.94	20	empty

Interfaces

3 interfaces between chains.

A–B · 741 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 191 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 92 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 30 disulfide (disulfide).

Compared structures

3TIH · Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 gp120 core · 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 3TIH · PDBe 3TIH

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