Research workbench
Crystal structure of L-N-carbamoylase from geobacillus stearothermophilus CECT43
Analyse Crystal structure of L-N-carbamoylase from geobacillus stearothermophilus CECT43 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N5F
- Type
- protein
- Length
- 812 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoyl-L-amino acid hydrolase
- EC
- 3.5.1.87
- UniProt
- Q53389
- Ligands
- CO
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-carbamoyl-L-amino acid hydrolase (EC 3.5.1.87) | protein | 406 | 37% helix, 24% strand | Q53389 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
- CAC · Cacodylate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.63 | 0.78 | 43 | CAC, CO |
| 2 | 296 | 0.52 | 0.74 | 45 | empty |
| 3 | 91 | 0.50 | 0.82 | 24 | IPA |
| 4 | 96 | 0.49 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 2221 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3N5F · Crystal Structure of L-N-carbamoylase from Geobacillus stearothermophilus CECT43 · the same entry in another collection · chain A against A, TM-score 1.00
- Q53389 · AlphaFold monomer V2.0 prediction for N-carbamoyl-L-amino acid hydrolase (Q53389) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q53389
- Elsewhere: RCSB PDB 3N5F · PDBe 3N5F · UniProt Q53389
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