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The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from bacillus anthracis str. sterne
Analyse The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DIB
- Type
- protein
- Length
- 2,554 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glyceraldehyde 3-phosphate dehydrogenase
- EC
- 1.2.1.12
- UniProt
- Q81L07
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 323 | 30% helix, 29% strand | Q81L07 |
| B, C | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 321 | 32% helix, 29% strand | Q81L07 |
| D | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 318 | 31% helix, 29% strand | Q81L07 |
| E | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 322 | 30% helix, 29% strand | Q81L07 |
| F | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 319 | 31% helix, 30% strand | Q81L07 |
| G | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 318 | 30% helix, 29% strand | Q81L07 |
| H | Glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.12) | protein | 312 | 29% helix, 30% strand | Q81L07 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, C, D, E, F, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.79 | 0.82 | 127 | empty |
| 2 | 757 | 0.72 | 0.78 | 103 | empty |
| 3 | 815 | 0.71 | 0.77 | 85 | empty |
| 4 | 396 | 0.62 | 0.77 | 51 | empty |
| 5 | 315 | 0.53 | 0.74 | 35 | empty |
Interfaces
17 interfaces between chains.
- B–C · 1908 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1907 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1896 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1876 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 545 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DIB · The crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Bacillus anthracis… · 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 Q81L07
- Elsewhere: RCSB PDB 4DIB · PDBe 4DIB · UniProt Q81L07
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