Research workbench
Wild-type glyceraldehyde dehydrogenase from thermoplasma acidophilum in complex with NADP
Analyse Wild-type glyceraldehyde dehydrogenase from thermoplasma acidophilum in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IZD
- Type
- protein
- Length
- 3,925 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glyceraldehyde dehydrogenase (NADP(+))
- EC
- 1.2.1.89
- UniProt
- Q9HK01
- Ligands
- NAP
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 494 | 41% helix, 22% strand | Q9HK01 |
| B, E, F, G, H | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 492 | 41% helix, 22% strand | Q9HK01 |
| C | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 484 | 41% helix, 21% strand | Q9HK01 |
| D | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 487 | 41% helix, 22% strand | Q9HK01 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.91 | 0.93 | 114 | empty |
| 2 | 1168 | 0.89 | 0.90 | 110 | empty |
| 3 | 545 | 0.81 | 0.87 | 73 | empty |
| 4 | 740 | 0.81 | 0.84 | 95 | empty |
| 5 | 628 | 0.80 | 0.85 | 76 | empty |
Interfaces
13 interfaces between chains.
- G–H · 4347 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 4314 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 4294 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 4266 Ų buried · 64 hydrogen bonds · protein-protein
- E–H · 1173 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 5IZD · Wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP · the same entry in another collection · chain H against H, TM-score 1.00
- Q9HK01 · AlphaFold monomer V2.0 prediction for D-glyceraldehyde dehydrogenase (NADP(+)) (Q9HK01) · a predicted model of the same protein · chain H 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 Q9HK01
- Elsewhere: RCSB PDB 5IZD · PDBe 5IZD · UniProt Q9HK01
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