MolNFT v1 · #61956 · protein
6-phosphogluconolactonase from plasmodium vivax
3E15 · Glucose-6-phosphate 1-dehydrogenase: “6-phosphogluconolactonase from plasmodium vivax”. X-ray diffraction, 3 ligands (K, AZI, CL), 15 pockets (best druggability 0.77). MolNFT v1 #61956 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3E15
- Type
- protein
- Length
- 1,176 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 3.1.1.31
- UniProt
- A5K3M1
- Ligands
- K, AZI, CL
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-6-phosphate 1-dehydrogenase (EC 3.1.1.31) | protein | 291 | 42% helix, 17% strand | A5K3M1 |
| B, C | Glucose-6-phosphate 1-dehydrogenase (EC 3.1.1.31) | protein | 295 | 46% helix, 16% strand | A5K3M1 |
| D | Glucose-6-phosphate 1-dehydrogenase (EC 3.1.1.31) | protein | 295 | 45% helix, 17% strand | A5K3M1 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- AZI · Azide ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 757 | 0.77 | 0.81 | 78 | CL |
| 2 | 128 | 0.51 | 0.81 | 21 | empty |
| 3 | 64 | 0.51 | 0.85 | 18 | empty |
| 4 | 61 | 0.50 | 0.84 | 17 | empty |
| 5 | 131 | 0.50 | 0.80 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1278 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 535 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 31 modified (engineered).
Compared structures
- 3E15 · 6-phosphogluconolactonase from Plasmodium vivax · 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 A5K3M1
- Elsewhere: RCSB PDB 3E15 · PDBe 3E15 · UniProt A5K3M1
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