Research workbench
Crystal structure analysis of N-carbamoyl-D-amino-acid amidohydrolase
Analyse Crystal structure analysis of N-carbamoyl-D-amino-acid amidohydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FO6
- Type
- protein
- Length
- 1,208 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoyl-D-amino-acid amidohydrolase
- EC
- 3.4.22.12
- UniProt
- Q44185
- Ligands
- XE
- Pockets
- 11 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-carbamoyl-D-amino-acid amidohydrolase (EC 3.4.22.12) | protein | 302 | 32% helix, 28% strand | Q44185 |
Ligands and binding sites
- XE · Xenon · ion · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.87 | 0.88 | 48 | empty |
| 2 | 285 | 0.79 | 0.91 | 45 | empty |
| 3 | 536 | 0.79 | 0.85 | 66 | empty |
| 4 | 542 | 0.78 | 0.85 | 75 | empty |
| 5 | 270 | 0.77 | 0.90 | 39 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2488 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2484 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 677 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 666 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FO6 · CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE · the same entry in another collection · chain D against D, TM-score 1.00
- Q44185 · AlphaFold monomer V2.0 prediction for N-carbamoyl-D-amino acid hydrolase (Q44185) · a predicted model of the same protein · 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 Q44185
- Elsewhere: RCSB PDB 1FO6 · PDBe 1FO6 · UniProt Q44185
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