MolNFT v1 · #157242 · protein
Crystal structure of BH1352 2-deoxyribose-5-phosphate from bacillus halodurans, K184L mutant
6MSW · Deoxyribose-phosphate aldolase: “Crystal structure of BH1352 2-deoxyribose-5-phosphate from bacillus halodurans, K184L mutant”. X-ray diffraction, 14 pockets (best druggability 0.77). MolNFT v1 #157242 on GenesisL1: 3D structure…
- PDB
- 6MSW
- Type
- protein
- Length
- 1,305 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
- 14 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 222 | 49% helix, 16% strand | Q9KD67 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 221 | 50% helix, 16% strand | Q9KD67 |
| C, D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 216 | 49% helix, 17% strand | Q9KD67 |
| E | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 217 | 47% helix, 17% strand | Q9KD67 |
| F | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 213 | 48% helix, 17% strand | Q9KD67 |
Ligands and binding sites
- GOL · Glycerol · additive · 17 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.77 | 0.99 | 24 | empty |
| 2 | 765 | 0.69 | 0.76 | 74 | GOL |
| 3 | 657 | 0.67 | 0.76 | 57 | GOL |
| 4 | 143 | 0.52 | 0.80 | 28 | empty |
| 5 | 131 | 0.52 | 0.81 | 22 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1315 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 450 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 437 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 427 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 99 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MSW · Crystal structure of BH1352 2-deoxyribose-5-phosphate from Bacillus halodurans, K184L… · 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 F 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 Q9KD67
- Elsewhere: RCSB PDB 6MSW · PDBe 6MSW · UniProt Q9KD67
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