Research workbench
Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from arthrobacter sp. at 2.0 ångströms resolution
Analyse Crystal structure analysis, refinement and enzymatic reaction mechanism of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NBA
- Type
- protein
- Length
- 1,011 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-carbamoylsarcosine amidohydrolase
- EC
- 3.5.1.59
- UniProt
- P32400
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | N-carbamoylsarcosine amidohydrolase (EC 3.5.1.59) | protein | 253 | 44% helix, 15% strand | P32400 |
| B | N-carbamoylsarcosine amidohydrolase (EC 3.5.1.59) | protein | 252 | 42% helix, 15% strand | P32400 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.87 | 0.94 | 50 | empty |
| 2 | 395 | 0.68 | 0.81 | 44 | empty |
| 3 | 376 | 0.67 | 0.80 | 38 | empty |
| 4 | 140 | 0.38 | 0.73 | 20 | empty |
| 5 | 68 | 0.32 | 0.75 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3618 Ų buried · 72 hydrogen bonds · protein-protein
- C–D · 3591 Ų buried · 68 hydrogen bonds · protein-protein
- B–D · 933 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 898 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 746 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1NBA · Crystal structure analysis, refinement and enzymatic reaction mechanism of… · the same entry in another collection · chain D against D, TM-score 1.00
- P32400 · AlphaFold monomer V2.0 prediction for N-carbamoylsarcosine amidase (P32400) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P32400
- Elsewhere: RCSB PDB 1NBA · PDBe 1NBA · UniProt P32400
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