Research workbench
Structure of cyclophilin complexed with sulfur-substituted tetrapeptide aapf
Analyse Structure of cyclophilin complexed with sulfur-substituted tetrapeptide aapf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VBT
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin a; Sulfur-substituted tetrapeptide
- UniProt
- P05092
- Ligands
- NIT
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclophilin a | protein | 164 | 14% helix, 32% strand | P05092 |
| C, D | Sulfur-substituted tetrapeptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NIT · 4-nitroaniline · ligand · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 226 | 0.53 | 0.76 | 29 | NIT |
| 2 | 84 | 0.36 | 0.76 | 21 | empty |
| 3 | 58 | 0.30 | 0.75 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–D · 247 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 241 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 193 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 58 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 57 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 1VBT · Structure of cyclophilin complexed with sulfur-substituted tetrapeptide AAPF · 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 P05092
- Elsewhere: RCSB PDB 1VBT · PDBe 1VBT · UniProt P05092
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