Research workbench
Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from streptococcus suis
Analyse Crystal structure of 2-deoxyribose-5-phosphate aldolase (1-220) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DBU
- Type
- protein
- Length
- 2,745 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- D5AHU8
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, I | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 211 | 45% helix, 17% strand | D5AHU8 |
| B, G | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 210 | 47% helix, 17% strand | D5AHU8 |
| D, K, L, M | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 212 | 46% helix, 17% strand | D5AHU8 |
| E | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 209 | 47% helix, 18% strand | D5AHU8 |
| F | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 210 | 43% helix, 16% strand | D5AHU8 |
| J | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 214 | 44% helix, 17% strand | D5AHU8 |
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.74 | 0.77 | 55 | empty |
| 2 | 476 | 0.67 | 0.78 | 69 | empty |
| 3 | 339 | 0.63 | 0.79 | 37 | empty |
| 4 | 301 | 0.61 | 0.79 | 35 | empty |
| 5 | 368 | 0.59 | 0.76 | 54 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1366 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 1365 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1363 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1350 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1348 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 D5AHU8
- Elsewhere: RCSB PDB 5DBU · PDBe 5DBU · UniProt D5AHU8
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