Research workbench
Crystal structure of proton-pumping pyrophosphatase
Analyse Crystal structure of proton-pumping pyrophosphatase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GPJ
- Type
- protein
- Length
- 2,914 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrophosphate-energized vacuolar membrane proton pump
- EC
- 3.6.1.1
- UniProt
- P21616
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 79% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) | protein | 732 | 81% helix, 2% strand | P21616 |
| B | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) | protein | 726 | 81% helix, 2% strand | P21616 |
| C | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) | protein | 728 | 78% helix, 2% strand | P21616 |
| D | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) | protein | 728 | 77% helix, 2% strand | P21616 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 926 | 0.76 | 0.79 | 102 | PO4, MG |
| 2 | 772 | 0.75 | 0.80 | 92 | empty |
| 3 | 736 | 0.73 | 0.79 | 84 | PO4, MG |
| 4 | 626 | 0.72 | 0.80 | 68 | PO4, MG |
| 5 | 52 | 0.72 | 0.99 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2998 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 2914 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 418 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 377 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5GPJ · Crystal Structure of Proton-Pumping Pyrophosphatase · the same entry in another collection · chain D against D, TM-score 1.00
- P21616 · AlphaFold monomer V2.0 prediction for pyrophosphate-energized vacuolar membrane proton… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P21616
- Elsewhere: RCSB PDB 5GPJ · PDBe 5GPJ · UniProt P21616
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