Research workbench
Crystal structure of amidase, HYDANTOINASE/CARBAMOYLASE family from burkholderia vietnamiensis
Analyse Crystal structure of amidase, HYDANTOINASE/CARBAMOYLASE family from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I4M
- Type
- protein
- Length
- 827 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amidase, HYDANTOINASE/CARBAMOYLASE family
- EC
- 3.5.1.87
- UniProt
- A4JQA0
- Ligands
- 3PG, ZN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidase, HYDANTOINASE/CARBAMOYLASE family (EC 3.5.1.87) | protein | 414 | 36% helix, 23% strand | A4JQA0 |
| B | Amidase, HYDANTOINASE/CARBAMOYLASE family (EC 3.5.1.87) | protein | 413 | 36% helix, 23% strand | A4JQA0 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.55 | 0.80 | 22 | empty |
| 2 | 155 | 0.53 | 0.80 | 24 | empty |
| 3 | 51 | 0.40 | 0.82 | 16 | empty |
| 4 | 106 | 0.35 | 0.73 | 22 | empty |
| 5 | 103 | 0.34 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2778 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5I4M · Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia… · 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 A4JQA0
- Elsewhere: RCSB PDB 5I4M · PDBe 5I4M · UniProt A4JQA0
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