Research workbench
Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma acidophilum
Analyse Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M4X
- Type
- protein
- Length
- 1,862 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.56
- Source
- Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155…
- Molecule
- D-glyceraldehyde dehydrogenase (NADP(+))
- EC
- 1.2.1.89
- UniProt
- Q9HK01
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.56 · 4 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 461 | 42% helix, 21% strand | Q9HK01 |
| B | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 468 | 41% helix, 22% strand | Q9HK01 |
| C | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 461 | 43% helix, 21% strand | Q9HK01 |
| D | D-glyceraldehyde dehydrogenase (NADP(+)) (EC 1.2.1.89) | protein | 472 | 42% helix, 22% strand | Q9HK01 |
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.84 | 0.91 | 73 | empty |
| 2 | 852 | 0.80 | 0.83 | 111 | empty |
| 3 | 532 | 0.71 | 0.80 | 73 | empty |
| 4 | 267 | 0.61 | 0.80 | 39 | empty |
| 5 | 326 | 0.60 | 0.78 | 41 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2848 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2605 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 579 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 204 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5M4X · Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from thermoplasma acidophilum · the same entry in another collection · chain D against D, TM-score 1.00
- Q9HK01 · AlphaFold monomer V2.0 prediction for D-glyceraldehyde dehydrogenase (NADP(+)) (Q9HK01) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 5M4X · PDBe 5M4X · UniProt Q9HK01
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