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Crystal structure of a HYDANTOINASE/CARBAMOYLASE family amidase from burkholderia ambifaria
Analyse Crystal structure of a HYDANTOINASE/CARBAMOYLASE family amidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TP4
- Type
- protein
- Length
- 814 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
- B1YW99
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amidase, HYDANTOINASE/CARBAMOYLASE family (EC 3.5.1.87) | protein | 405 | 38% helix, 24% strand | B1YW99 |
| B | Amidase, HYDANTOINASE/CARBAMOYLASE family (EC 3.5.1.87) | protein | 409 | 38% helix, 24% strand | B1YW99 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- FMT · Formic acid · additive · 7 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.62 | 0.77 | 57 | ZN, MES, EDO, FMT |
| 2 | 382 | 0.59 | 0.76 | 50 | ZN, MES, EDO |
| 3 | 107 | 0.52 | 0.82 | 22 | empty |
| 4 | 97 | 0.43 | 0.79 | 20 | empty |
| 5 | 53 | 0.32 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2249 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5TP4 · Crystal structure of a hydantoinase/carbamoylase family amidase 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 B1YW99
- Elsewhere: RCSB PDB 5TP4 · PDBe 5TP4 · UniProt B1YW99
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