MolNFT v1 · #171564 · protein
Escherichia COLI D-2-deoxyribose-5-phosphate aldolase - C47V/G204A/S239D mutant
6Z9H · Deoxyribose-phosphate aldolase: “Escherichia COLI D-2-deoxyribose-5-phosphate aldolase - C47V/G204A/S239D mutant”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.66). MolNFT v1 #171564 on GenesisL1: 3D structure…
- PDB
- 6Z9H
- Type
- protein
- Length
- 496 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- E2QLE1
- Ligands
- MG
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 50% helix, 16% strand | E2QLE1 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- FMT · Formic acid · additive · chains A
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 | 224 | 0.66 | 0.84 | 31 | empty |
| 2 | 203 | 0.62 | 0.82 | 29 | empty |
| 3 | 84 | 0.46 | 0.82 | 21 | EDO |
| 4 | 63 | 0.46 | 0.84 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 666 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6Z9H · Escherichia coli D-2-deoxyribose-5-phosphate aldolase - C47V/G204A/S239D mutant · 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 6Z9H · PDBe 6Z9H · UniProt E2QLE1
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