Research workbench
Crystal structure of NADH pyrophosphatase (ec 3.6.1.22) (1790429) from escherichia COLI K12 at 2.30 a resolution
Analyse Crystal structure of NADH pyrophosphatase (ec 3.6.1.22) (1790429) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GB5
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.22
- UniProt
- P32664
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH pyrophosphatase (EC 3.6.1.22) | protein | 265 | 21% helix, 38% strand | P32664 |
| B | NADH pyrophosphatase (EC 3.6.1.22) | protein | 261 | 22% helix, 37% strand | P32664 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 887 | 0.85 | 0.86 | 108 | empty |
| 2 | 169 | 0.55 | 0.80 | 27 | empty |
| 3 | 119 | 0.41 | 0.76 | 28 | empty |
| 4 | 83 | 0.40 | 0.78 | 15 | empty |
| 5 | 131 | 0.38 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2164 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 2GB5 · Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli… · 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 B 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 P32664
- Elsewhere: RCSB PDB 2GB5 · PDBe 2GB5 · UniProt P32664
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