Research workbench
Crystal structure of phosphoenolpyruvate mutase complexed with MG(II)
Analyse Crystal structure of phosphoenolpyruvate mutase complexed with MG(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S2V
- Type
- protein
- Length
- 1,132 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate phosphomutase
- EC
- 5.4.2.9
- UniProt
- P56839
- Ligands
- MG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 282 | 50% helix, 12% strand | P56839 |
| B | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 287 | 48% helix, 12% strand | P56839 |
| C | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 282 | 48% helix, 12% strand | P56839 |
| D | Phosphoenolpyruvate phosphomutase (EC 5.4.2.9) | protein | 281 | 49% helix, 12% strand | P56839 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.83 | 0.95 | 44 | empty |
| 2 | 551 | 0.73 | 0.81 | 42 | MG |
| 3 | 682 | 0.73 | 0.79 | 60 | MG |
| 4 | 71 | 0.73 | 0.97 | 19 | empty |
| 5 | 677 | 0.73 | 0.79 | 46 | MG |
Interfaces
6 interfaces between chains.
- B–C · 3546 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 3430 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1165 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 816 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1S2V · Crystal structure of phosphoenolpyruvate mutase complexed with Mg(II) · the same entry in another collection · chain D against D, TM-score 1.00
- P56839 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate phosphomutase (P56839) · a predicted model of the same protein · chain D 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 1S2V · PDBe 1S2V · UniProt P56839
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