MolNFT v1 · #118520 · protein
HIV-1 GP120 complex with jp-III-048
5F4L · Envelope glycoprotein GP120 of HIV-1 clade C: “HIV-1 GP120 complex with jp-III-048”. X-ray diffraction, 1 ligand (5VE), 4 pockets (best druggability 0.76). MolNFT v1 #118520 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5F4L
- 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
- 5VE
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 336 | 17% helix, 40% strand | — |
| B | Envelope glycoprotein GP120 of HIV-1 clade C | protein | 335 | 17% helix, 38% strand | — |
Ligands and binding sites
- 5VE · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-6-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.76 | 0.78 | 115 | empty |
| 2 | 93 | 0.59 | 0.87 | 25 | 5VE |
| 3 | 73 | 0.58 | 0.89 | 19 | 5VE |
| 4 | 51 | 0.29 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 370 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5F4L · HIV-1 gp120 complex with JP-III-048 · 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 5F4L · PDBe 5F4L
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