MolNFT v1 · #103925 · protein
Crystal structure of yeast METHYLGLYOXAL/ISOVALERALDEHYDE reductase GRE2 complexed with NADPH
4PVD · NADPH-dependent methylglyoxal reductase GRE2: “Crystal structure of yeast METHYLGLYOXAL/ISOVALERALDEHYDE reductase GRE2 complexed with NADPH”. X-ray diffraction, 1 ligand (NDP), 14 pockets (best druggability 0.77). MolNFT v1 #103925…
- PDB
- 4PVD
- Type
- protein
- Length
- 1,297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-dependent methylglyoxal reductase GRE2
- EC
- 1.1.1.283, 1.1.1.265
- UniProt
- Q12068
- Ligands
- NDP
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADPH-dependent methylglyoxal reductase GRE2 (EC 1.1.1.283, 1.1.1.265) | protein | 342 | 42% helix, 16% strand | Q12068 |
| C | NADPH-dependent methylglyoxal reductase GRE2 (EC 1.1.1.283, 1.1.1.265) | protein | 308 | 40% helix, 18% strand | Q12068 |
| D | NADPH-dependent methylglyoxal reductase GRE2 (EC 1.1.1.283, 1.1.1.265) | protein | 305 | 40% helix, 18% strand | Q12068 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.77 | 0.79 | 84 | NDP |
| 2 | 729 | 0.76 | 0.81 | 65 | NDP |
| 3 | 434 | 0.66 | 0.79 | 62 | empty |
| 4 | 315 | 0.53 | 0.74 | 36 | empty |
| 5 | 132 | 0.47 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- B–D · 565 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 147 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 31 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4PVD · Crystal structure of yeast methylglyoxal/isovaleraldehyde reductase Gre2 complexed with… · the same entry in another collection · chain B against B, TM-score 1.00
- Q12068 · AlphaFold monomer V2.0 prediction for NADPH-dependent methylglyoxal reductase GRE2… · 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 Q12068
- Elsewhere: RCSB PDB 4PVD · PDBe 4PVD · UniProt Q12068
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