MolNFT v1 · #25256 · protein
Crystal structure of NADH pyrophosphatase (1790429) from escherichia COLI K12 at 2.20 a resolution
1VK6: “Crystal structure of NADH pyrophosphatase (1790429) from escherichia COLI K12 at 2.20 a resolution”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.73). MolNFT v1 #25256 on GenesisL1: 3D structure, binding sites…
- PDB
- 1VK6
- Type
- protein
- Length
- 257 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.-
- UniProt
- P32664
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH pyrophosphatase (EC 3.6.1.-) | protein | 257 | 23% helix, 38% strand | P32664 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.73 | 0.82 | 39 | MPD |
| 2 | 107 | 0.43 | 0.77 | 15 | MPD |
| 3 | 62 | 0.38 | 0.79 | 11 | MPD |
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 1VK6 · Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A… · the same entry in another collection · chain A against A, TM-score 1.00
- P32664 · AlphaFold monomer V2.0 prediction for NAD-capped RNA hydrolase nudc (P32664) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 P32664
- Elsewhere: RCSB PDB 1VK6 · PDBe 1VK6 · UniProt P32664
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