Research workbench
Crystal structure of a deoxyribose-phosphate aldolase (TM_1559) from thermotoga maritima at 1.83 a resolution
Analyse Crystal structure of a deoxyribose-phosphate aldolase (TM_1559) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R13
- Type
- protein
- Length
- 515 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
- Q9X1P5
- Ligands
- UNL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 257 | 53% helix, 14% strand | Q9X1P5 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 258 | 53% helix, 14% strand | Q9X1P5 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · 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 | 177 | 0.56 | 0.80 | 27 | UNL, GOL |
| 2 | 167 | 0.55 | 0.80 | 26 | UNL, GOL |
| 3 | 57 | 0.30 | 0.75 | 12 | empty |
| 4 | 57 | 0.27 | 0.73 | 12 | ACT |
Interfaces
1 interface between chains.
- A–B · 1521 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 3R13 · Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1P5 · AlphaFold monomer V2.0 prediction for deoxyribose-phosphate aldolase (Q9X1P5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9X1P5
- Elsewhere: RCSB PDB 3R13 · PDBe 3R13 · UniProt Q9X1P5
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