Research workbench
Crystal structure of deoxyribose phosphate aldolase from mycobacterium smegmatis
Analyse Crystal structure of deoxyribose phosphate aldolase from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NDO
- Type
- protein
- Length
- 450 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
- A0QQY7
- Ligands
- UNL, NH4
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 225 | 48% helix, 16% strand | A0QQY7 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.58 | 0.88 | 33 | empty |
| 2 | 143 | 0.52 | 0.80 | 25 | UNL |
| 3 | 127 | 0.50 | 0.80 | 23 | UNL |
| 4 | 53 | 0.35 | 0.79 | 18 | empty |
| 5 | 72 | 0.35 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1177 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3NDO · Crystal structure of deoxyribose phosphate aldolase from mycobacterium smegmatis · 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 A0QQY7
- Elsewhere: RCSB PDB 3NDO · PDBe 3NDO · UniProt A0QQY7
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