Research workbench
Crystal structure of methylglyoxal synthase from elizabethkingia anophelis NUHP1
Analyse Crystal structure of methylglyoxal synthase from elizabethkingia anophelis NUHP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PHE
- Type
- protein
- Length
- 1,817 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylglyoxal synthase
- EC
- 4.2.3.3
- UniProt
- A0A077EEZ5
- Ligands
- PO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, H, I, J, K, L | Methylglyoxal synthase (EC 4.2.3.3) | protein | 151 | 44% helix, 18% strand | A0A077EEZ5 |
| B, C, E, F, G | Methylglyoxal synthase (EC 4.2.3.3) | protein | 152 | 43% helix, 19% strand | A0A077EEZ5 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 12 copies · chains A, F, B, C, D, E, G, L, H, I, J, K
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.84 | 0.85 | 156 | empty |
| 2 | 1133 | 0.80 | 0.82 | 154 | empty |
| 3 | 216 | 0.61 | 0.81 | 31 | empty |
| 4 | 209 | 0.60 | 0.81 | 33 | empty |
| 5 | 177 | 0.60 | 0.82 | 29 | empty |
Interfaces
25 interfaces between chains.
- K–L · 1612 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1587 Ų buried · 21 hydrogen bonds · protein-protein
- I–J · 1572 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1569 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1567 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6PHE · Crystal structure of Methylglyoxal synthase from Elizabethkingia anophelis NUHP1 · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A077EEZ5
- Elsewhere: RCSB PDB 6PHE · PDBe 6PHE · UniProt A0A077EEZ5
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