MolNFT v1 · #56269 · protein
Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin
2ZA0: “Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin”. X-ray diffraction, 2 ligands (MGI, ZN), 4 pockets (best druggability 0.63). MolNFT v1 #56269 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2ZA0
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyoxalase I
- EC
- 4.4.1.5
- UniProt
- A5GZX3
- Ligands
- MGI, ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyoxalase I (EC 4.4.1.5) | protein | 180 | 28% helix, 27% strand | A5GZX3 |
| B | Glyoxalase I (EC 4.4.1.5) | protein | 176 | 29% helix, 28% strand | A5GZX3 |
Ligands and binding sites
- MGI · methyl 4-(2,3-dihydroxy-5-methylphenoxy)-2-hydroxy-6-methylbenzoate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.63 | 0.79 | 33 | MGI |
| 2 | 251 | 0.61 | 0.80 | 26 | MGI |
| 3 | 119 | 0.42 | 0.76 | 22 | empty |
| 4 | 89 | 0.35 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3756 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 2ZA0 · Crystal structure of mouse glyoxalase I complexed with methyl-gerfelin · 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 A5GZX3
- Elsewhere: RCSB PDB 2ZA0 · PDBe 2ZA0 · UniProt A5GZX3
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