MolNFT v1 · #187625 · protein
Structure of G6PD-D200N tetramer bound to NADP+ and G6P
7SNI · Glucose-6-phosphate 1-dehydrogenase: “Structure of G6PD-D200N tetramer bound to NADP+ and G6P”. Electron microscopy, 2 ligands (NAP, BG6), 20 pockets (best druggability 0.87). MolNFT v1 #187625 on GenesisL1: 3D structure, binding…
- PDB
- 7SNI
- Type
- protein
- Length
- 1,952 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 1.1.1.49
- UniProt
- P11413
- Ligands
- NAP, BG6
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 488 | 38% helix, 21% strand | P11413 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
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 | 1139 | 0.87 | 0.88 | 82 | empty |
| 2 | 695 | 0.76 | 0.81 | 80 | NAP |
| 3 | 712 | 0.76 | 0.81 | 74 | NAP |
| 4 | 660 | 0.69 | 0.77 | 67 | NAP, BG6 |
| 5 | 635 | 0.69 | 0.77 | 63 | NAP, BG6 |
Interfaces
6 interfaces between chains.
- C–D · 3286 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3285 Ų buried · 62 hydrogen bonds · protein-protein
- A–C · 491 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 490 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 306 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7SNI · Structure of G6PD-D200N tetramer bound to NADP+ and G6P · the same entry in another collection · chain D against D, TM-score 1.00
- P11413 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate 1-dehydrogenase (P11413) · 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 P11413
- Elsewhere: RCSB PDB 7SNI · PDBe 7SNI · UniProt P11413
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