Research workbench
HIV-1 GP120 complex with bnm-IV-197
Analyse HIV-1 GP120 complex with bnm-IV-197 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F4U
- Type
- protein
- Length
- 671 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
- 5VH, NAG
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 335 | 15% helix, 36% strand | — |
| B | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 336 | 18% helix, 40% strand | — |
Ligands and binding sites
- 5VH · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-[[carbamimidoyl(methyl)amino]methyl]-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1172 | 0.75 | 0.78 | 117 | NAG |
| 2 | 79 | 0.59 | 0.88 | 19 | 5VH |
| 3 | 94 | 0.58 | 0.87 | 25 | 5VH |
| 4 | 178 | 0.56 | 0.81 | 33 | empty |
| 5 | 53 | 0.39 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5F4U · HIV-1 gp120 complex with BNM-IV-197 · 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 5F4U · PDBe 5F4U
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.