MolNFT v1 · #48629 · protein
NAD+ synthetase from bacillus anthracis with AMP-cpp and MG2+
2PZ8 · NH(3)-dependent NAD(+) synthetase: “NAD+ synthetase from bacillus anthracis with AMP-cpp and MG2+”. X-ray diffraction, 2 ligands (APC, MG), 3 pockets (best druggability 0.84). MolNFT v1 #48629 on GenesisL1: 3D structure, binding…
- PDB
- 2PZ8
- Type
- protein
- Length
- 560 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
- Q81RP3
- Ligands
- APC, MG
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NH(3)-dependent NAD(+) synthetase (EC 6.3.1.5) | protein | 280 | 53% helix, 8% strand | Q81RP3 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.84 | 0.88 | 79 | MG, APC, GOL |
| 2 | 720 | 0.84 | 0.87 | 80 | MG, APC, GOL |
| 3 | 491 | 0.77 | 0.85 | 60 | empty |
Interfaces
1 interface between chains.
- A–B · 3073 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 2PZ8 · NAD+ Synthetase from Bacillus anthracis with AMP-CPP and Mg2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q81RP3 · AlphaFold monomer V2.0 prediction for NH(3)-dependent NAD(+) synthetase (Q81RP3) · a predicted model of the same protein · chain A 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 Q81RP3
- Elsewhere: RCSB PDB 2PZ8 · PDBe 2PZ8 · UniProt Q81RP3
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