Research workbench
Crystal structure of methylglyoxal synthase from thermus thermophilus HB8
Analyse Crystal structure of methylglyoxal synthase from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WO8
- Type
- protein
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylglyoxal synthase
- EC
- 4.2.3.3
- UniProt
- Q5SHD6
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylglyoxal synthase (EC 4.2.3.3) | protein | 126 | 51% helix, 16% strand | Q5SHD6 |
| B, C, D, F | Methylglyoxal synthase (EC 4.2.3.3) | protein | 123 | 52% helix, 17% strand | Q5SHD6 |
| E | Methylglyoxal synthase (EC 4.2.3.3) | protein | 122 | 52% helix, 16% strand | Q5SHD6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1143 | 0.88 | 0.89 | 100 | empty |
| 2 | 76 | 0.42 | 0.80 | 20 | SO4 |
| 3 | 78 | 0.41 | 0.79 | 20 | SO4 |
| 4 | 74 | 0.40 | 0.79 | 20 | SO4 |
| 5 | 68 | 0.39 | 0.80 | 21 | SO4 |
Interfaces
12 interfaces between chains.
- C–D · 945 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 933 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 916 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 771 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 765 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1WO8 · Crystal structure of methylglyoxal synthase from Thermus thermophilus HB8 · the same entry in another collection · chain F against F, TM-score 1.00
- Q5SHD6 · AlphaFold monomer V2.0 prediction for methylglyoxal synthase (Q5SHD6) · 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 Q5SHD6
- Elsewhere: RCSB PDB 1WO8 · PDBe 1WO8 · UniProt Q5SHD6
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