Research workbench
Molecular structure for the HIV-1 GP120 trimer in the CD4-bound state
Analyse Molecular structure for the HIV-1 GP120 trimer in the CD4-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNO
- 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
- 8 · 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
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.74 | 0.98 | 33 | empty |
| 2 | 65 | 0.72 | 0.98 | 33 | empty |
| 3 | 99 | 0.61 | 0.88 | 22 | empty |
| 4 | 100 | 0.61 | 0.87 | 25 | empty |
| 5 | 88 | 0.60 | 0.88 | 22 | empty |
Interfaces
9 interfaces between chains.
- E–F · 3927 Ų buried · 71 hydrogen bonds · protein-protein
- H–I · 3915 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 3914 Ų buried · 71 hydrogen bonds · protein-protein
- G–H · 1427 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1426 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 3DNO · Molecular structure for the HIV-1 gp120 trimer in the CD4-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 3DNO · PDBe 3DNO · UniProt P04578
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