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Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase
Analyse Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZCO
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-dehydro-3-deoxyphosphoheptonate aldolase
- EC
- 4.1.2.15
- UniProt
- Q8U0A9
- Ligands
- PEP, MN, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 2-dehydro-3-deoxyphosphoheptonate aldolase (EC 4.1.2.15) | protein | 262 | 37% helix, 18% strand | Q8U0A9 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.66 | 0.87 | 28 | CL, PEP |
| 2 | 133 | 0.57 | 0.84 | 23 | CL, PEP |
| 3 | 73 | 0.38 | 0.78 | 16 | empty |
| 4 | 62 | 0.35 | 0.77 | 16 | empty |
| 5 | 77 | 0.27 | 0.71 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1ZCO · Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate 7-phosphate… · the same entry in another collection · chain B against B, 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 1ZCO · PDBe 1ZCO · UniProt Q8U0A9
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