MolNFT v1 · #14188 · protein
Crystal structure of phosphoenolpyruvate mutase complexed with sulfopyruvate
1M1B · Phosphoenolpyruvate phosphomutase: “Crystal structure of phosphoenolpyruvate mutase complexed with sulfopyruvate”. X-ray diffraction, 2 ligands (SPV, MG), 6 pockets (best druggability 0.68). MolNFT v1 #14188 on GenesisL1: 3D…
- PDB
- 1M1B
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate phosphomutase
- EC
- 5.4.2.9
- UniProt
- P56839
- Ligands
- SPV, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 291 | 47% helix, 13% strand | P56839 |
| B | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 289 | 49% helix, 13% strand | P56839 |
Ligands and binding sites
- SPV · Sulfopyruvate · ligand · 2 copies · chains A, B
- MG · Magnesium 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.68 | 0.95 | 17 | MG, SPV |
| 2 | 55 | 0.67 | 0.96 | 18 | MG, SPV |
| 3 | 113 | 0.55 | 0.83 | 22 | empty |
| 4 | 401 | 0.55 | 0.73 | 45 | empty |
| 5 | 157 | 0.39 | 0.73 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1175 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1M1B · Crystal Structure of Phosphoenolpyruvate Mutase Complexed with Sulfopyruvate · the same entry in another collection · chain B against B, TM-score 1.00
- P56839 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate phosphomutase (P56839) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P56839
- Elsewhere: RCSB PDB 1M1B · PDBe 1M1B · UniProt P56839
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