MolNFT v1 · #122664 · protein
Crystal structure of E. COLI nudc in complex with nmn
5IW5 · NADH pyrophosphatase: “Crystal structure of E. COLI nudc in complex with nmn”. X-ray diffraction, 2 ligands (NMN, ZN), 4 pockets (best druggability 0.75). MolNFT v1 #122664 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5IW5
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.22
- UniProt
- D6JHV3
- Ligands
- NMN, ZN
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | NADH pyrophosphatase (EC 3.6.1.22) | protein | 256 | 21% helix, 38% strand | D6JHV3 |
| A | NADH pyrophosphatase (EC 3.6.1.22) | protein | 254 | 21% helix, 38% strand | D6JHV3 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · 2 copies · chains B, A
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1034 | 0.75 | 0.78 | 83 | empty |
| 2 | 521 | 0.71 | 0.80 | 39 | NMN |
| 3 | 477 | 0.64 | 0.77 | 37 | NMN |
| 4 | 51 | 0.32 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- B–A · 341 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5IW5 · Crystal structure of E. coli NudC in complex with NMN · the same entry in another collection · chain B against B, 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 D6JHV3
- Elsewhere: RCSB PDB 5IW5 · PDBe 5IW5 · UniProt D6JHV3
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