Research workbench
Crystal structure of deoxyribose-phosphate aldolase from shewanella halifaxensis
Analyse Crystal structure of deoxyribose-phosphate aldolase from shewanella halifaxensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C6M
- Type
- protein
- Length
- 989 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- B0TQ91
- Ligands
- NA, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 49% helix, 15% strand | B0TQ91 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 49% helix, 15% strand | B0TQ91 |
| C | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 50% helix, 15% strand | B0TQ91 |
| D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 50% helix, 16% strand | B0TQ91 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 448 | 0.70 | 0.81 | 48 | NA, CL |
| 2 | 730 | 0.69 | 0.76 | 80 | empty |
| 3 | 428 | 0.67 | 0.79 | 49 | CL |
| 4 | 101 | 0.50 | 0.82 | 24 | empty |
| 5 | 92 | 0.48 | 0.82 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 679 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 621 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 134 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 132 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5C6M · Crystal structure of deoxyribose-phosphate aldolase from Shewanella halifaxensis · the same entry in another collection · chain D against D, TM-score 1.00
- B0TQ91 · AlphaFold monomer V2.0 prediction for deoxyribose-phosphate aldolase (B0TQ91) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 B0TQ91
- Elsewhere: RCSB PDB 5C6M · PDBe 5C6M · UniProt B0TQ91
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