MolNFT v1 · #46974 · protein
Crystal strcture of human prolidase
2OKN · Xaa-pro dipeptidase: “Crystal strcture of human prolidase”. X-ray diffraction, 2 ligands (MN, PI), 7 pockets (best druggability 0.83). MolNFT v1 #46974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OKN
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidase
- EC
- 3.4.13.9
- UniProt
- P12955
- Ligands
- MN, PI
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 477 | 38% helix, 17% strand | P12955 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- PI · Hydrogenphosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.83 | 0.86 | 73 | empty |
| 2 | 802 | 0.82 | 0.85 | 87 | PI |
| 3 | 1171 | 0.80 | 0.82 | 114 | MN, PI |
| 4 | 74 | 0.47 | 0.83 | 27 | empty |
| 5 | 71 | 0.43 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 3037 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
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 P12955
- Elsewhere: RCSB PDB 2OKN · PDBe 2OKN · UniProt P12955
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