MolNFT v1 · #184914 · protein
Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric michael addition reactions, schiff base complex with cinnamaldehyde
7P76 · Deoxyribose-phosphate aldolase: “Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric michael addition reactions, schiff…”. X-ray diffraction, 1 ligand (9Y6), 20 pockets (best druggability 0.76). MolNFT v1…
- PDB
- 7P76
- Type
- protein
- Length
- 2,964 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyribose-phosphate aldolase
- EC
- 4.1.2.4
- UniProt
- V0AAC4
- Ligands
- 9Y6
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 9 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 49% helix, 16% strand | V0AAC4 |
| B | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 50% helix, 16% strand | V0AAC4 |
| C, F, G | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 50% helix, 15% strand | V0AAC4 |
| D | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 49% helix, 16% strand | V0AAC4 |
| E | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 248 | 49% helix, 16% strand | V0AAC4 |
| H, I | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 50% helix, 16% strand | V0AAC4 |
| J | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 51% helix, 16% strand | V0AAC4 |
| K | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 247 | 49% helix, 16% strand | V0AAC4 |
| L | Deoxyribose-phosphate aldolase (EC 4.1.2.4) | protein | 246 | 50% helix, 15% strand | V0AAC4 |
Ligands and binding sites
- 9Y6 · (2E)-3-phenylprop-2-enal · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- GOL · Glycerol · additive · chains I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.76 | 0.82 | 74 | 9Y6 |
| 2 | 833 | 0.75 | 0.79 | 75 | 9Y6 |
| 3 | 1122 | 0.75 | 0.78 | 85 | 9Y6 |
| 4 | 628 | 0.73 | 0.80 | 61 | 9Y6 |
| 5 | 294 | 0.73 | 0.86 | 44 | 9Y6 |
Interfaces
23 interfaces between chains.
- F–I · 636 Ų buried · 2 hydrogen bonds · protein-protein
- E–H · 629 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 613 Ų buried · 1 hydrogen bond · protein-protein
- A–L · 612 Ų buried · 2 hydrogen bonds · protein-protein
- D–G · 598 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 covalent (covalent ligand).
Compared structures
- 7P76 · Re-engineered 2-deoxy-D-ribose-5-phosphate aldolase catalysing asymmetric Michael… · the same entry in another collection · chain E against E, 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 V0AAC4
- Elsewhere: RCSB PDB 7P76 · PDBe 7P76 · UniProt V0AAC4
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