MolNFT v1 · #14438 · protein
X-ray crystal structure of cyclophilin A/HIV-1 ca N-terminal domain (1-146) M-type H87A complex.
1M9E: “X-ray crystal structure of cyclophilin A/HIV-1 ca N-terminal domain (1-146) M-type H87A complex.”. X-ray diffraction, 4 pockets (best druggability 0.74). MolNFT v1 #14438 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1M9E
- Type
- protein
- Length
- 607 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin a; HIV-1 capsid
- EC
- 5.2.1.8
- UniProt
- P62937, Q72497
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclophilin a (EC 5.2.1.8) | protein | 164 | 14% helix, 30% strand | P62937 |
| B | Cyclophilin a (EC 5.2.1.8) | protein | 162 | 15% helix, 33% strand | P62937 |
| C | HIV-1 capsid | protein | 146 | 56% helix, 4% strand | Q72497 |
| D | HIV-1 capsid | protein | 135 | 61% helix, 0% strand | Q72497 |
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 | 656 | 0.74 | 0.80 | 51 | empty |
| 2 | 336 | 0.61 | 0.78 | 43 | empty |
| 3 | 262 | 0.52 | 0.75 | 34 | empty |
| 4 | 58 | 0.30 | 0.75 | 12 | empty |
Interfaces
4 interfaces between chains.
- B–C · 554 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 401 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 392 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1M9E · X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A… · 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 P62937
- Every structure of UniProt Q72497
- Elsewhere: RCSB PDB 1M9E · PDBe 1M9E · UniProt P62937 · UniProt Q72497
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