Research workbench
Structure of NAD synthetase from vibrio cholerae
Analyse Structure of NAD synthetase from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q4G
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- C3NY23
- Ligands
- CA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 266 | 56% helix, 8% strand | C3NY23 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 257 | 57% helix, 8% strand | C3NY23 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.81 | 0.86 | 79 | empty |
| 2 | 530 | 0.76 | 0.83 | 55 | CA |
| 3 | 363 | 0.61 | 0.78 | 49 | empty |
| 4 | 268 | 0.60 | 0.79 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 2705 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3Q4G · Structure of NAD synthetase from Vibrio cholerae · 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 C3NY23
- Elsewhere: RCSB PDB 3Q4G · PDBe 3Q4G · UniProt C3NY23
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