MolNFT v1 · #87444 · protein
Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase
4C1K · 2-dehydro-3-deoxyphosphoheptonate aldolase: “Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase”. X-ray diffraction, 4 ligands (PEP, CD, CO3), 19 pockets (best druggability 0.75). MolNFT…
- PDB
- 4C1K
- Type
- protein
- Length
- 1,572 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphoheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- Q8U0A9
- Ligands
- PEP, CD, CO3, CL
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 2-dehydro-3-deoxyphosphoheptonate aldolase (EC 2.5.1.54) | protein | 262 | 39% helix, 18% strand | Q8U0A9 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 6 copies · chains A, B, C, D, E, F
- CD · Cadmium ion · metal · 6 copies · chains A, B, C, D, E, F
- CO3 · Carbonate ion · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains E, F
- 2PE · Nonaethylene glycol · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 68 | 0.75 | 0.99 | 18 | empty |
| 2 | 67 | 0.73 | 0.98 | 18 | empty |
| 3 | 1066 | 0.72 | 0.76 | 80 | CO3, PEP |
| 4 | 276 | 0.63 | 0.81 | 52 | PEP, CO3 |
| 5 | 86 | 0.58 | 0.88 | 20 | CO3, PEP |
Interfaces
11 interfaces between chains.
- A–B · 1475 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1462 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1281 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1279 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1277 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4C1K · Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate… · the same entry in another collection · chain A 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 Q8U0A9
- Elsewhere: RCSB PDB 4C1K · PDBe 4C1K · UniProt Q8U0A9
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