Research workbench
X-ray crystal structure of cyclophilin A/HIV-1 ca N-terminal domain (1-146) M-type H87A,G89A complex.
Analyse X-ray crystal structure of cyclophilin A/HIV-1 ca N-terminal domain (1-146)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M9Y
- Type
- protein
- Length
- 1,220 residues
- Chains
- 8
- 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
- 9 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Cyclophilin a (EC 5.2.1.8) | protein | 165 | 14% helix, 31% strand | P62937 |
| B, F | Cyclophilin a (EC 5.2.1.8) | protein | 164 | 14% helix, 31% strand | P62937 |
| C, G | HIV-1 capsid | protein | 146 | 57% helix, 4% strand | Q72497 |
| D, H | HIV-1 capsid | protein | 135 | 62% helix, 1% strand | Q72497 |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.74 | 0.77 | 98 | empty |
| 2 | 746 | 0.74 | 0.79 | 58 | empty |
| 3 | 498 | 0.61 | 0.75 | 41 | empty |
| 4 | 349 | 0.60 | 0.77 | 41 | empty |
| 5 | 396 | 0.60 | 0.76 | 44 | empty |
Interfaces
9 interfaces between chains.
- B–C · 558 Ų buried · 8 hydrogen bonds · protein-protein
- F–G · 518 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 435 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 422 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1M9Y · X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type… · 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 1M9Y · PDBe 1M9Y · UniProt P62937 · UniProt Q72497
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