Research workbench
Crystal structure of BH1352 2-deoxyribose-5-phosphate from bacillus halodurans
Analyse Crystal structure of BH1352 2-deoxyribose-5-phosphate from bacillus halodurans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D33
- Type
- protein
- Length
- 1,307 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- Q9KD67
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 6 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 224 | 48% helix, 17% strand | Q9KD67 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 216 | 49% helix, 17% strand | Q9KD67 |
| C | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 213 | 49% helix, 16% strand | Q9KD67 |
| D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 216 | 48% helix, 17% strand | Q9KD67 |
| E | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 217 | 49% helix, 17% strand | Q9KD67 |
| F | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 221 | 49% helix, 16% strand | Q9KD67 |
Ligands and binding sites
- GOL · Glycerol · additive · 14 copies · chains A, C, B, E, D, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains B, E, A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.77 | 0.99 | 26 | empty |
| 2 | 78 | 0.77 | 0.99 | 24 | empty |
| 3 | 81 | 0.77 | 0.99 | 24 | empty |
| 4 | 1023 | 0.71 | 0.75 | 70 | GOL, TRS |
| 5 | 678 | 0.67 | 0.76 | 60 | TRS, GOL |
Interfaces
5 interfaces between chains.
- A–B · 1353 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1340 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1316 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 427 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6D33 · Crystal structure of BH1352 2-deoxyribose-5-phosphate from Bacillus halodurans · the same entry in another collection · chain F against F, TM-score 1.00
- Q9KD67 · AlphaFold monomer V2.0 prediction for deoxyribose-phosphate aldolase (Q9KD67) · a predicted model of the same protein · chain C 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 Q9KD67
- Elsewhere: RCSB PDB 6D33 · PDBe 6D33 · UniProt Q9KD67
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