MolNFT v1 · #145921 · protein
Glucose-6-P dehydrogenase (apo form) from trypanosoma cruzi
6D23 · Glucose-6-phosphate 1-dehydrogenase: “Glucose-6-P dehydrogenase (apo form) from trypanosoma cruzi”. X-ray diffraction, 2 ligands (SO4, CL), 20 pockets (best druggability 0.88). MolNFT v1 #145921 on GenesisL1: 3D structure, binding…
- PDB
- 6D23
- Type
- protein
- Length
- 1,965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 1.1.1.49
- UniProt
- Q1WBU6
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 487 | 37% helix, 21% strand | Q1WBU6 |
| B | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 490 | 38% helix, 20% strand | Q1WBU6 |
| C, D | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 494 | 37% helix, 21% strand | Q1WBU6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, D, C
- CL · Chloride ion · ion · 23 copies · chains A, D, B, C
- GOL · Glycerol · additive · 20 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.88 | 0.89 | 101 | GOL |
| 2 | 775 | 0.70 | 0.77 | 76 | SO4, GOL |
| 3 | 766 | 0.70 | 0.76 | 82 | SO4, GOL |
| 4 | 793 | 0.70 | 0.76 | 82 | SO4, GOL, CL |
| 5 | 612 | 0.67 | 0.76 | 81 | SO4, GOL |
Interfaces
6 interfaces between chains.
- B–C · 2602 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 2582 Ų buried · 41 hydrogen bonds · protein-protein
- A–B · 572 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 572 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6D23 · Glucose-6-P dehydrogenase (apo form) from trypanosoma cruzi · 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 Q1WBU6
- Elsewhere: RCSB PDB 6D23 · PDBe 6D23 · UniProt Q1WBU6
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