MolNFT v1 · #57037 · protein
Dimeric 6-phosphogluconate dehydrogenase complexed with glucose
2ZYD · 6-phosphogluconate dehydrogenase, decarboxylating: “Dimeric 6-phosphogluconate dehydrogenase complexed with glucose”. X-ray diffraction, 1 ligand (GLO), 7 pockets (best druggability 0.79). MolNFT v1 #57037 on GenesisL1: 3D…
- PDB
- 2ZYD
- Type
- protein
- Length
- 930 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- UniProt
- P00350
- Ligands
- GLO
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 464 | 57% helix, 10% strand | P00350 |
| B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 466 | 58% helix, 11% strand | P00350 |
Ligands and binding sites
- GLO · D-glucose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.98 | 38 | empty |
| 2 | 367 | 0.73 | 0.84 | 41 | empty |
| 3 | 434 | 0.72 | 0.82 | 48 | GLO |
| 4 | 227 | 0.51 | 0.76 | 26 | empty |
| 5 | 188 | 0.48 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 5524 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 2ZYD · Dimeric 6-phosphogluconate dehydrogenase complexed with glucose · the same entry in another collection · chain A against A, TM-score 1.00
- P00350 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · 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 P00350
- Elsewhere: RCSB PDB 2ZYD · PDBe 2ZYD · UniProt P00350
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