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Crystal structure of amidase, HYDANTOINASE/CARBAMOYLASE family from burkholderia multivorans
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
- 5THW
- Type
- protein
- Length
- 1,647 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deacylase
- EC
- 3.5.1.87
- UniProt
- A0A0H3KRF1
- Ligands
- URP, ZN
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deacylase (EC 3.5.1.87) | protein | 412 | 36% helix, 23% strand | A0A0H3KRF1 |
| B | Deacylase (EC 3.5.1.87) | protein | 412 | 36% helix, 23% strand | A0A0H3KRF1 |
| D | Deacylase (EC 3.5.1.87) | protein | 411 | 36% helix, 23% strand | A0A0H3KRF1 |
Ligands and binding sites
- URP · N-(aminocarbonyl)-beta-alanine · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.79 | 0.82 | 93 | empty |
| 2 | 398 | 0.67 | 0.80 | 46 | empty |
| 3 | 332 | 0.65 | 0.80 | 32 | empty |
| 4 | 132 | 0.52 | 0.80 | 22 | empty |
| 5 | 57 | 0.50 | 0.86 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2509 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2460 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 453 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 124 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5THW · 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 A0A0H3KRF1
- Elsewhere: RCSB PDB 5THW · PDBe 5THW · UniProt A0A0H3KRF1
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