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Cyrstal structure of human cyclophilin-a in complex with suc-agpf-pna
Analyse Cyrstal structure of human cyclophilin-a in complex with suc-agpf-pna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZKF
- Type
- protein
- Length
- 337 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase a; Suc-ala-gly-pro-phe-pna
- EC
- 5.2.1.8
- UniProt
- P62937
- Ligands
- NIT
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 165 | 14% helix, 32% strand | P62937 |
| B | Peptidyl-prolyl cis-trans isomerase a (EC 5.2.1.8) | protein | 164 | 14% helix, 32% strand | P62937 |
| C, D | Suc-ala-gly-pro-phe-pna | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NIT · 4-nitroaniline · ligand · 2 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 2 copies · chains A, C, B, 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 | 255 | 0.57 | 0.78 | 30 | NIT |
| 2 | 50 | 0.28 | 0.75 | 18 | empty |
| 3 | 56 | 0.26 | 0.73 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 276 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 275 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 190 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 101 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (additive adduct, covalent ligand).
Compared structures
- 1ZKF · Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA · 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
- Elsewhere: RCSB PDB 1ZKF · PDBe 1ZKF · UniProt P62937
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