MolNFT v1 · #85039 · protein
Crystal structure of the H-translocating pyrophosphatase
4A01 · Proton pyrophosphatase: “Crystal structure of the H-translocating pyrophosphatase”. X-ray diffraction, 3 ligands (2PN, MG, K), 15 pockets (best druggability 0.76). MolNFT v1 #85039 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4A01
- Type
- protein
- Length
- 1,480 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proton pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- O22124
- Ligands
- 2PN, MG, K
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proton pyrophosphatase (EC 3.6.1.1) | protein | 740 | 82% helix, 3% strand | O22124 |
Ligands and binding sites
- 2PN · Imidodiphosphoric acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 10 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- DMU · Decyl-beta-D-maltopyranoside · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.76 | 0.98 | 34 | MG, K, 2PN |
| 2 | 93 | 0.74 | 0.97 | 32 | MG, K, 2PN |
| 3 | 244 | 0.73 | 0.87 | 43 | empty |
| 4 | 60 | 0.73 | 0.98 | 17 | empty |
| 5 | 341 | 0.71 | 0.84 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 3318 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4A01 · Crystal Structure of the H-Translocating Pyrophosphatase · 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 O22124
- Elsewhere: RCSB PDB 4A01 · PDBe 4A01 · UniProt O22124
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