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Crystal structure of tetrameric structure of aldolase from thermus thermophilus HB8
Analyse Crystal structure of tetrameric structure of aldolase from thermus thermophilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UB3
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldolase protein
- EC
- 4.1.2.4
- UniProt
- Q7SIC8
- Ligands
- HPD
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aldolase protein (EC 4.1.2.4) | protein | 211 | 48% helix, 17% strand | Q7SIC8 |
| B | Aldolase protein (EC 4.1.2.4) | protein | 211 | 47% helix, 17% strand | Q7SIC8 |
| C | Aldolase protein (EC 4.1.2.4) | protein | 210 | 48% helix, 17% strand | Q7SIC8 |
Ligands and binding sites
- HPD · 1-hydroxy-pentane-3,4-diol-5-phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.69 | 0.84 | 50 | empty |
| 2 | 158 | 0.48 | 0.78 | 20 | empty |
| 3 | 111 | 0.47 | 0.80 | 26 | HPD |
| 4 | 75 | 0.46 | 0.82 | 22 | HPD |
| 5 | 68 | 0.46 | 0.83 | 20 | HPD |
Interfaces
6 interfaces between chains.
- A–C · 1568 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1561 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 523 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 515 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 104 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1UB3 · Crystal Structure of Tetrameric Structure of Aldolase from thermus thermophilus HB8 · 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 Q7SIC8
- Elsewhere: RCSB PDB 1UB3 · PDBe 1UB3 · UniProt Q7SIC8
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