MolNFT v1 · #26730 · protein
Crystal structure of the prolidase from pyrococcus horikoshii OT3
1WY2 · Xaa-pro dipeptidase: “Crystal structure of the prolidase from pyrococcus horikoshii OT3”. X-ray diffraction, 2 ligands (ZN, MG), 5 pockets (best druggability 0.76). MolNFT v1 #26730 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1WY2
- Type
- protein
- Length
- 698 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
- O58885
- Ligands
- ZN, MG
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 351 | 39% helix, 25% strand | O58885 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 347 | 39% helix, 24% strand | O58885 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.76 | 0.79 | 99 | empty |
| 2 | 661 | 0.72 | 0.79 | 63 | CAC, GOL |
| 3 | 519 | 0.64 | 0.76 | 44 | CAC |
| 4 | 88 | 0.35 | 0.75 | 15 | empty |
| 5 | 60 | 0.34 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1822 Ų buried · 18 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 O58885
- Elsewhere: RCSB PDB 1WY2 · PDBe 1WY2 · UniProt O58885
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