Research workbench
Crystal structure of D-hydantoinase from bacillus sp. AR9 in C2221 space group
Analyse Crystal structure of D-hydantoinase from bacillus sp. AR9 in C2221 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KIR
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-hydantoinase
- EC
- 3.5.2.2
- UniProt
- Q5DLU2
- Ligands
- MN
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-hydantoinase (EC 3.5.2.2) | protein | 460 | 32% helix, 23% strand | Q5DLU2 |
| B | D-hydantoinase (EC 3.5.2.2) | protein | 456 | 34% helix, 23% strand | Q5DLU2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.76 | 0.93 | 31 | empty |
| 2 | 200 | 0.59 | 0.81 | 24 | empty |
| 3 | 182 | 0.58 | 0.81 | 22 | empty |
| 4 | 91 | 0.54 | 0.85 | 17 | empty |
| 5 | 79 | 0.49 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1125 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4KIR · Crystal Structure of D-Hydantoinase from Bacillus sp. AR9 in C2221 space group · 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 Q5DLU2
- Elsewhere: RCSB PDB 4KIR · PDBe 4KIR · UniProt Q5DLU2
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