MolNFT v1 · #155044 · protein
Crystal structure of NAD+ synthetase from staphylococcus aureus
6KV3 · NH(3)-dependent NAD(+) synthetase: “Crystal structure of NAD+ synthetase from staphylococcus aureus”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #155044 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6KV3
- Type
- protein
- Length
- 992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NH(3)-dependent NAD(+) synthetase
- EC
- 6.3.1.5
- UniProt
- Q5HEK9
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 249 | 54% helix, 8% strand | Q5HEK9 |
| C | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 248 | 52% helix, 8% strand | Q5HEK9 |
| B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 252 | 52% helix, 8% strand | Q5HEK9 |
| D | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 243 | 52% helix, 9% strand | Q5HEK9 |
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.72 | 0.81 | 65 | empty |
| 2 | 558 | 0.70 | 0.79 | 64 | empty |
| 3 | 483 | 0.67 | 0.79 | 58 | empty |
| 4 | 573 | 0.63 | 0.75 | 54 | empty |
| 5 | 308 | 0.61 | 0.79 | 44 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2628 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2581 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 128 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 117 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6KV3 · Crystal Structure of NAD+ Synthetase from Staphylococcus aureus · the same entry in another collection · chain D against D, TM-score 1.00
- Q5HEK9 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q5HEK9) · a predicted model of the same protein · chain A 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 Q5HEK9
- Elsewhere: RCSB PDB 6KV3 · PDBe 6KV3 · UniProt Q5HEK9
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