Research workbench
Structure of the HIV-1 GP41 membrane-proximal ectodomain region in a putative prefusion conformation
Analyse Structure of the HIV-1 GP41 membrane-proximal ectodomain region in a putative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 6 hydrogen bonds · protein-protein
- D–F · 831 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 811 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 791 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 791 Ų 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.