Research workbench
X-ray structure of methylglyoxal synthase from E. COLI complexed with phosphoglycolohydroxamic acid
Analyse X-ray structure of methylglyoxal synthase from E. COLI complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IK4
- Type
- protein
- Length
- 910 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylglyoxal synthase
- EC
- 4.2.3.3
- UniProt
- P0A731
- Ligands
- PGH
- Pockets
- 12 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Methylglyoxal synthase (EC 4.2.3.3) | protein | 152 | 49% helix, 21% strand | P0A731 |
| B, F | Methylglyoxal synthase (EC 4.2.3.3) | protein | 151 | 49% helix, 21% strand | P0A731 |
Ligands and binding sites
- PGH · Phosphoglycolohydroxamic acid · ligand · 6 copies · chains A, F, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1199 | 0.88 | 0.89 | 114 | empty |
| 2 | 243 | 0.69 | 0.85 | 29 | empty |
| 3 | 246 | 0.68 | 0.84 | 30 | empty |
| 4 | 200 | 0.68 | 0.86 | 20 | empty |
| 5 | 264 | 0.67 | 0.83 | 30 | empty |
Interfaces
12 interfaces between chains.
- B–E · 1459 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1453 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1451 Ų buried · 29 hydrogen bonds · protein-protein
- C–F · 1303 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1278 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1IK4 · X-ray Structure of Methylglyoxal Synthase from E. coli Complexed with… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A731 · AlphaFold monomer V2.0 prediction for methylglyoxal synthase (P0A731) · 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 P0A731
- Elsewhere: RCSB PDB 1IK4 · PDBe 1IK4 · UniProt P0A731
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