MolNFT v1 · #24958 · protein
Pyruvate phosphate dikinase with bound mg-pep from maize
1VBH · PYRUVATE,ORTHOPHOSPHATE dikinase: “Pyruvate phosphate dikinase with bound mg-pep from maize”. X-ray diffraction, 3 ligands (PEP, MG, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #24958 on GenesisL1: 3D structure, binding…
- PDB
- 1VBH
- Type
- protein
- Length
- 862 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PYRUVATE,ORTHOPHOSPHATE dikinase
- EC
- 2.7.9.1
- UniProt
- P11155
- Ligands
- PEP, MG, SO4
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PYRUVATE,ORTHOPHOSPHATE dikinase (EC 2.7.9.1) | protein | 862 | 47% helix, 17% strand | P11155 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.72 | 0.76 | 80 | MG, PEP |
| 2 | 141 | 0.56 | 0.82 | 28 | empty |
| 3 | 243 | 0.53 | 0.76 | 34 | empty |
| 4 | 162 | 0.41 | 0.73 | 27 | empty |
| 5 | 84 | 0.33 | 0.74 | 24 | empty |
Compared structures
- 1VBH · Pyruvate Phosphate Dikinase with bound Mg-PEP from Maize · the same entry in another collection · chain A against A, TM-score 1.00
- P11155 · AlphaFold monomer V2.0 prediction for pyruvate, phosphate dikinase 1, chloroplastic… · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P11155
- Elsewhere: RCSB PDB 1VBH · PDBe 1VBH · UniProt P11155
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