MolNFT v1 · #171040 · protein
Crystal structure of ATP-dependent caprolactamase from pseudomonas jessenii
6YRA · Hydantoinase: “Crystal structure of ATP-dependent caprolactamase from pseudomonas jessenii”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.86). MolNFT v1 #171040 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YRA
- Type
- protein
- Length
- 2,540 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydantoinase; 5-oxoprolinase
- UniProt
- A0A2W0FH34, A0A2W0EVE0
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | Hydantoinase | protein | 579 | 30% helix, 21% strand | A0A2W0FH34 |
| A, C | 5-oxoprolinase | protein | 691 | 31% helix, 21% strand | A0A2W0EVE0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.86 | 0.88 | 124 | empty |
| 2 | 696 | 0.86 | 0.90 | 105 | empty |
| 3 | 103 | 0.79 | 0.98 | 23 | empty |
| 4 | 317 | 0.78 | 0.89 | 53 | empty |
| 5 | 91 | 0.78 | 0.98 | 24 | empty |
Interfaces
3 interfaces between chains.
- D–C · 3085 Ų buried · 29 hydrogen bonds · protein-protein
- B–A · 2948 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 1278 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6YRA · Crystal structure of ATP-dependent caprolactamase from Pseudomonas jessenii · the same entry in another collection · chain B against B, 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 A0A2W0FH34
- Every structure of UniProt A0A2W0EVE0
- Elsewhere: RCSB PDB 6YRA · PDBe 6YRA · UniProt A0A2W0FH34 · UniProt A0A2W0EVE0
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