MolNFT v1 · #64651 · protein

Structure of the HIV-1 GP41 membrane-proximal ectodomain region in a putative prefusion conformation

3G9R · Fusion complex of HIV-1 envelope glycoprotein and…: “Structure of the HIV-1 GP41 membrane-proximal ectodomain region in a putative prefusion conformation”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.81).…

PDB: 3G9R
Type: protein
Length: 244 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fusion complex of HIV-1 envelope glycoprotein and saccharomyces cerevisiae general…
UniProt: Q4QX39, P03069
Ligands: PO4
Pockets: 7 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 94% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fusion complex of HIV-1 envelope glycoprotein and saccharomyces cerevisiae general control protein GCN4	protein	42	95% helix, 0% strand	Q4QX39, P03069
B, C, E	Fusion complex of HIV-1 envelope glycoprotein and saccharomyces cerevisiae general control protein GCN4	protein	40	95% helix, 0% strand	Q4QX39, P03069
D, F	Fusion complex of HIV-1 envelope glycoprotein and saccharomyces cerevisiae general control protein GCN4	protein	41	93% helix, 0% strand	Q4QX39, P03069

Ligands and binding sites

PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains A, B, C, E, F, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	487	0.81	0.88	37	empty
2	69	0.73	0.97	16	MPD
3	361	0.58	0.76	30	MPD
4	73	0.44	0.81	14	empty
5	72	0.39	0.79	16	empty

Interfaces

9 interfaces between chains.

B–C · 832 Å² buried · 6 hydrogen bonds · protein-protein
D–F · 831 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 811 Å² buried · 5 hydrogen bonds · protein-protein
D–E · 791 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 791 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3G9R · Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion… · the same entry in another collection · chain F against F, TM-score 1.00
P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain A against A, TM-score 0.86

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 Q4QX39
Every structure of UniProt P03069
Elsewhere: RCSB PDB 3G9R · PDBe 3G9R · UniProt Q4QX39 · UniProt P03069

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