MolNFT v1 · #89138 · protein
Trimcyp cyclophilin domain from macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex
4DGE: “Trimcyp cyclophilin domain from macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex”. X-ray diffraction, 6 pockets (best druggability 0.76). MolNFT v1 #89138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4DGE
- Type
- protein
- Length
- 609 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trimcyp; Capsid protein
- EC
- 5.2.1.8
- UniProt
- B0LJC8, Q72497
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trimcyp (EC 5.2.1.8) | protein | 164 | 14% helix, 32% strand | B0LJC8 |
| C | Capsid protein | protein | 136 | 60% helix, 1% strand | Q72497 |
| D | Capsid protein | protein | 145 | 57% helix, 4% strand | Q72497 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.76 | 0.80 | 64 | empty |
| 2 | 227 | 0.54 | 0.77 | 33 | empty |
| 3 | 99 | 0.49 | 0.82 | 26 | empty |
| 4 | 151 | 0.47 | 0.77 | 22 | empty |
| 5 | 85 | 0.39 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- B–D · 638 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 514 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 481 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DGE · TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex · 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 B0LJC8
- Every structure of UniProt Q72497
- Elsewhere: RCSB PDB 4DGE · PDBe 4DGE · UniProt B0LJC8 · UniProt Q72497
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