MolNFT v1 · #21386 · protein
H98N mutant of methylglyoxal synthase from E. COLI complexed with phosphoglycolic acid
1S89: “H98N mutant of methylglyoxal synthase from E. COLI complexed with phosphoglycolic acid”. X-ray diffraction, 1 ligand (PGA), 13 pockets (best druggability 0.88). MolNFT v1 #21386 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1S89
- Type
- protein
- Length
- 912 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
- PGA
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Methylglyoxal synthase (EC 4.2.3.3) | protein | 152 | 47% helix, 21% strand | P0A731 |
Ligands and binding sites
- PGA · 2-phosphoglycolic 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
13 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.88 | 0.89 | 130 | empty |
| 2 | 330 | 0.67 | 0.81 | 36 | empty |
| 3 | 219 | 0.64 | 0.83 | 33 | empty |
| 4 | 208 | 0.64 | 0.83 | 34 | empty |
| 5 | 171 | 0.62 | 0.83 | 21 | empty |
Interfaces
12 interfaces between chains.
- A–F · 1555 Ų buried · 30 hydrogen bonds · protein-protein
- B–E · 1530 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1496 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1281 Ų buried · 16 hydrogen bonds · protein-protein
- C–F · 1248 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1S89 · H98N Mutant of Methylglyoxal Synthase from E. coli complexed with Phosphoglycolic Acid · the same entry in another collection · chain C against C, TM-score 1.00
- P0A731 · AlphaFold monomer V2.0 prediction for methylglyoxal synthase (P0A731) · a predicted model of the same protein · chain A 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 1S89 · PDBe 1S89 · UniProt P0A731
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