Research workbench
Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant complex with reaction products
Analyse Escherichia coli D-2-deoxyribose-5-phosphate aldolase - N21K mutant complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Z9I
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.86
- Source
- Escherichia coli
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- E2QLE1
- Ligands
- G3H, MG
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.86 · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 50% helix, 15% strand | E2QLE1 |
Ligands and binding sites
- G3H · Glyceraldehyde-3-phosphate · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.63 | 0.83 | 29 | empty |
| 2 | 199 | 0.61 | 0.82 | 25 | empty |
| 3 | 108 | 0.50 | 0.81 | 22 | EDO |
| 4 | 72 | 0.48 | 0.84 | 19 | G3H |
Interfaces
1 interface between chains.
- A–B · 663 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6Z9I · Escherichia COLI D-2-deoxyribose-5-phosphate aldolase - N21K mutant complex with reaction… · 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 E2QLE1
- Elsewhere: RCSB PDB 6Z9I · PDBe 6Z9I · UniProt E2QLE1
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