MolNFT v1 · #118526 · protein
HIV-1 GP120 complex with bnw-IV-147
5F4R · Envelope glycoprotein GP120 of HIV-1 clade C: “HIV-1 GP120 complex with bnw-IV-147”. X-ray diffraction, 2 ligands (5VF, NAG), 7 pockets (best druggability 0.76). MolNFT v1 #118526 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F4R
- Type
- protein
- Length
- 670 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein GP120 of HIV-1 clade C
- Ligands
- 5VF, NAG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 335 | 16% helix, 37% strand | — |
Ligands and binding sites
- 5VF · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C
- FMT · Formic acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.76 | 0.79 | 96 | NAG |
| 2 | 89 | 0.59 | 0.87 | 22 | 5VF |
| 3 | 84 | 0.58 | 0.87 | 22 | 5VF |
| 4 | 178 | 0.54 | 0.79 | 28 | NAG |
| 5 | 89 | 0.39 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 396 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 5F4R · HIV-1 gp120 complex with BNW-IV-147 · 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 5F4R · PDBe 5F4R
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