Research workbench
Cyclophilin a stabilize HIV-1 capsid through a novel non- canonical binding site
Analyse Cyclophilin a stabilize HIV-1 capsid through a novel non- canonical binding site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJB
- Type
- protein
- Length
- 600 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gag polyprotein; Peptidyl-prolyl cis-trans isomerase a
- EC
- 5.2.1.8
- UniProt
- P03347, P62937
- Pockets
- 6 · best druggability 0.53
Structure
electron microscopy · 2 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gag polyprotein | protein | 218 | 60% helix, 2% strand | P03347 |
| C | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 164 | 14% helix, 30% strand | P62937 |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.53 | 0.75 | 36 | empty |
| 2 | 76 | 0.39 | 0.77 | 15 | empty |
| 3 | 62 | 0.37 | 0.79 | 15 | empty |
| 4 | 60 | 0.36 | 0.78 | 19 | empty |
| 5 | 66 | 0.34 | 0.76 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–C · 503 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 113 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5FJB · Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site · the same entry in another collection · chain B against B, 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 P03347
- Every structure of UniProt P62937
- Elsewhere: RCSB PDB 5FJB · PDBe 5FJB · UniProt P03347 · UniProt P62937
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