MolNFT v1 · #176994 · protein
Crystal structure of nudc complexed with dpcoa
7E44 · NADH pyrophosphatase: “Crystal structure of nudc complexed with dpcoa”. X-ray diffraction, 2 ligands (COD, ZN), 10 pockets (best druggability 0.84). MolNFT v1 #176994 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7E44
- Type
- protein
- Length
- 1,013 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH pyrophosphatase
- EC
- 3.6.1.22
- UniProt
- A0A140SS78
- Ligands
- COD, ZN
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADH pyrophosphatase (EC 3.6.1.22) | protein | 256 | 23% helix, 39% strand | A0A140SS78 |
| B | NADH pyrophosphatase (EC 3.6.1.22) | protein | 244 | 23% helix, 36% strand | A0A140SS78 |
| E | NADH pyrophosphatase (EC 3.6.1.22) | protein | 257 | 23% helix, 39% strand | A0A140SS78 |
| F | NADH pyrophosphatase (EC 3.6.1.22) | protein | 256 | 22% helix, 39% strand | A0A140SS78 |
Ligands and binding sites
- COD · Dephospho coenzyme A · ligand · 2 copies · chains E, F
- ZN · Zinc ion · metal · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1133 | 0.84 | 0.85 | 104 | COD |
| 2 | 1033 | 0.78 | 0.80 | 88 | empty |
| 3 | 464 | 0.78 | 0.86 | 72 | empty |
| 4 | 317 | 0.62 | 0.79 | 32 | COD |
| 5 | 186 | 0.48 | 0.76 | 32 | empty |
Interfaces
3 interfaces between chains.
- E–F · 1678 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 977 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7E44 · Crystal structure of NudC complexed with dpCoA · the same entry in another collection · chain A against A, 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 A0A140SS78
- Elsewhere: RCSB PDB 7E44 · PDBe 7E44 · UniProt A0A140SS78
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