MolNFT v1 · #118524 · protein
HIV-1 GP120 complex with bnm-III-170
5F4P · Envelope glycoprotein GP120 of HIV-1 clade C: “HIV-1 GP120 complex with bnm-III-170”. X-ray diffraction, 2 ligands (5VG, NAG), 5 pockets (best druggability 0.77). MolNFT v1 #118524 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F4P
- 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
- 5VG, NAG
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 335 | 16% helix, 39% strand | — |
Ligands and binding sites
- 5VG · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · 2 copies · chains D, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.77 | 0.79 | 105 | NAG |
| 2 | 91 | 0.61 | 0.88 | 23 | 5VG |
| 3 | 75 | 0.58 | 0.88 | 21 | 5VG |
| 4 | 81 | 0.41 | 0.79 | 17 | empty |
| 5 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- D–A · 286 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5F4P · HIV-1 gp120 complex with BNM-III-170 · 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 5F4P · PDBe 5F4P
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.