Research workbench
Crystal structure of NAD synthetase nade from vibrio fischeri
Analyse Crystal structure of NAD synthetase nade from vibrio fischeri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WP0
- Type
- protein
- Length
- 534 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
- Q5DZX4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 260 | 55% helix, 8% strand | Q5DZX4 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 274 | 52% helix, 7% strand | Q5DZX4 |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.76 | 0.80 | 82 | empty |
| 2 | 620 | 0.70 | 0.78 | 49 | empty |
| 3 | 401 | 0.62 | 0.77 | 37 | empty |
| 4 | 334 | 0.60 | 0.78 | 47 | empty |
| 5 | 93 | 0.38 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2579 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5WP0 · Crystal structure of NAD synthetase NadE from Vibrio fischeri · the same entry in another collection · chain B against B, TM-score 1.00
- Q5DZX4 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q5DZX4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q5DZX4
- Elsewhere: RCSB PDB 5WP0 · PDBe 5WP0 · UniProt Q5DZX4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.