MolNFT v1 · #61507 · protein
Molecular structure for the HIV-1 GP120 trimer in the B12-bound state
3DNL · HIV-1 envelope glycoprotein GP120: “Molecular structure for the HIV-1 GP120 trimer in the B12-bound state”. Electron microscopy, 9 pockets (best druggability 0.74). MolNFT v1 #61507 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DNL
- Type
- protein
- Length
- 864 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HIV-1 envelope glycoprotein GP120
- UniProt
- P04578
- Pockets
- 9 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 15% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | HIV-1 envelope glycoprotein GP120 | protein | 35 | 43% helix, 17% strand | P04578 |
| B, E, H | HIV-1 envelope glycoprotein GP120 | protein | 170 | 12% helix, 35% strand | P04578 |
| C, F, I | HIV-1 envelope glycoprotein GP120 | protein | 83 | 10% helix, 45% strand | P04578 |
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.74 | 0.98 | 33 | empty |
| 2 | 69 | 0.73 | 0.98 | 33 | empty |
| 3 | 58 | 0.72 | 0.98 | 27 | empty |
| 4 | 94 | 0.63 | 0.89 | 22 | empty |
| 5 | 74 | 0.60 | 0.89 | 21 | empty |
Interfaces
9 interfaces between chains.
- H–I · 3920 Ų buried · 71 hydrogen bonds · protein-protein
- E–F · 3917 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 3908 Ų buried · 71 hydrogen bonds · protein-protein
- D–E · 1421 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1421 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3DNL · Molecular structure for the HIV-1 gp120 trimer in the b12-bound state · 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
- Every structure of UniProt P04578
- Elsewhere: RCSB PDB 3DNL · PDBe 3DNL · UniProt P04578
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