MolNFT v1 · #24926 · protein
Structure of E. COLI cyclophilin B K163T mutant bound to N-acetyl-ala- ala-pro-ala-7-amino-4-methylcoumarin
1VAI: “Structure of E. COLI cyclophilin B K163T mutant bound to N-acetyl-ala- ala-pro-ala-7-amino-4-methylcoumarin”. X-ray diffraction, 2 ligands (ACE, MCM), 1 pocket (best druggability 0.31). MolNFT v1 #24926 on GenesisL1: 3D structure…
- PDB
- 1VAI
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclophilin B; (ACE)AAPA(MCM)
- EC
- 5.2.1.8
- UniProt
- P20752
- Ligands
- ACE, MCM
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclophilin B (EC 5.2.1.8) | protein | 166 | 16% helix, 34% strand | P20752 |
| C | (ACE)AAPA(MCM) | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, C
- MCM · 7-amino-4-methyl-chromen-2-one · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.31 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- B–C · 286 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1VAI · Structure of e. coli cyclophilin B K163T mutant bound to… · 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 P20752
- Elsewhere: RCSB PDB 1VAI · PDBe 1VAI · UniProt P20752
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