MolNFT v1 · #37915 · protein
The mutant A302C of agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase
2GGK · N-carbamoyl-D-amino acid amidohydrolase: “The mutant A302C of agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase”. X-ray diffraction, 12 pockets (best druggability 0.87). MolNFT v1 #37915 on GenesisL1: 3D structure…
- PDB
- 2GGK
- 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
- 3.5.1.77
- UniProt
- Q44185
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | N-carbamoyl-D-amino acid amidohydrolase (EC 3.5.1.77) | protein | 302 | 32% helix, 29% strand | Q44185 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.87 | 0.88 | 49 | empty |
| 2 | 560 | 0.80 | 0.86 | 68 | empty |
| 3 | 581 | 0.79 | 0.85 | 74 | empty |
| 4 | 266 | 0.78 | 0.91 | 39 | empty |
| 5 | 283 | 0.78 | 0.90 | 42 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2523 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2509 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 680 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 671 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2GGK · The mutant A302C of Agrobacterium radiobacter 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 D 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 2GGK · PDBe 2GGK · UniProt Q44185
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