Research workbench
Crystal structure of a deoxyribose-phosphate aldolase (TM_1559) from thermotoga maritima at 1.75 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
- 3R12
- Type
- protein
- Length
- 510 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
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 255 | 53% helix, 15% strand | Q9X1P5 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, B
- PGO · S-1,2-propanediol · additive · chains A
- GOL · Glycerol · 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 | 104 | 0.56 | 0.85 | 22 | CIT |
| 2 | 113 | 0.54 | 0.83 | 26 | CIT |
| 3 | 61 | 0.29 | 0.73 | 12 | empty |
| 4 | 54 | 0.27 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1504 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3R12 · 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 B against A, TM-score 0.97
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 3R12 · PDBe 3R12 · UniProt Q9X1P5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.