MolNFT v1 · #169520 · protein
Crystal structure of the tetrameric 6-phosphogluconate dehydrogenase from gluconobacter oxidans
6XEQ: “Crystal structure of the tetrameric 6-phosphogluconate dehydrogenase from gluconobacter oxidans”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.79). MolNFT v1 #169520 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XEQ
- Type
- protein
- Length
- 1,271 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- EC
- 1.1.1.343
- UniProt
- G5EBD7
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase (EC 1.1.1.343) | protein | 320 | 49% helix, 13% strand | G5EBD7 |
| B | 6-phosphogluconate dehydrogenase (EC 1.1.1.343) | protein | 318 | 50% helix, 13% strand | G5EBD7 |
| C | 6-phosphogluconate dehydrogenase (EC 1.1.1.343) | protein | 318 | 53% helix, 13% strand | G5EBD7 |
| D | 6-phosphogluconate dehydrogenase (EC 1.1.1.343) | protein | 315 | 52% helix, 13% strand | G5EBD7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.79 | 0.88 | 44 | empty |
| 2 | 681 | 0.71 | 0.79 | 55 | empty |
| 3 | 608 | 0.70 | 0.79 | 50 | empty |
| 4 | 433 | 0.66 | 0.79 | 47 | SO4 |
| 5 | 428 | 0.63 | 0.77 | 61 | SO4 |
Interfaces
6 interfaces between chains.
- A–D · 3737 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 3681 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 1888 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1858 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 844 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6XEQ · Crystal structure of the tetrameric 6-phosphogluconate dehydrogenase from Gluconobacter… · the same entry in another collection · chain D against D, TM-score 1.00
- G5EBD7 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, NAD(+)-dependent… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 G5EBD7
- Elsewhere: RCSB PDB 6XEQ · PDBe 6XEQ · UniProt G5EBD7
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