Research workbench
Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from bacillus halodurans C-125 complexed with NADP
Analyse Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RHH
- Type
- protein
- Length
- 1,907 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.9
- UniProt
- Q9KAQ0
- Ligands
- NAP, SO4
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 475 | 41% helix, 24% strand | Q9KAQ0 |
| B | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 476 | 41% helix, 25% strand | Q9KAQ0 |
| C | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 476 | 42% helix, 23% strand | Q9KAQ0 |
| D | NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.9) | protein | 480 | 41% helix, 23% strand | Q9KAQ0 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 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
17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1139 | 0.87 | 0.88 | 119 | empty |
| 2 | 800 | 0.85 | 0.88 | 96 | empty |
| 3 | 475 | 0.79 | 0.87 | 55 | empty |
| 4 | 332 | 0.79 | 0.90 | 39 | empty |
| 5 | 316 | 0.78 | 0.89 | 41 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2661 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2630 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 948 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 627 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3RHH · Crystal structure of NADP-dependent glyceraldehyde-3-phosphate dehydrogenase from… · 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 Q9KAQ0
- Elsewhere: RCSB PDB 3RHH · PDBe 3RHH · UniProt Q9KAQ0
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