Research workbench
Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii at 3.00 A resolution
Analyse Structure of erythrose-4-phosphate dehydrogenase from Acinetobacter baumannii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ZN1
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Acinetobacter baumannii
- Molecule
- Glyceraldehyde-3-phosphate dehydrogenase
- EC
- 1.2.1.-
- UniProt
- A0A059ZTK9
- Ligands
- NAD, SO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · resolution 3 · 1 distinct chain · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.-) | protein | 341 | 28% helix, 30% strand | A0A059ZTK9 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, D, C, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.81 | 0.82 | 119 | empty |
| 2 | 631 | 0.74 | 0.81 | 51 | NAD, SO4 |
| 3 | 647 | 0.74 | 0.80 | 51 | NAD, SO4 |
| 4 | 640 | 0.73 | 0.80 | 50 | NAD, SO4 |
| 5 | 576 | 0.72 | 0.81 | 51 | NAD, SO4 |
Interfaces
6 interfaces between chains.
- C–D · 2006 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1982 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- C–B · 1273 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 558 Ų buried · 9 hydrogen bonds · protein-protein
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 A0A059ZTK9
- Elsewhere: RCSB PDB 8ZN1 · PDBe 8ZN1 · UniProt A0A059ZTK9
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