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The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with GLY190PRO mutation
Analyse The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBJ
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospho-2-dehydro-3-deoxyheptonate aldolase
- EC
- 2.5.1.54
- UniProt
- A0A0T9FW33
- Ligands
- MN, SO4, CL, PO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 444 | 45% helix, 14% strand | A0A0T9FW33 |
| B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 416 | 48% helix, 14% strand | A0A0T9FW33 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.79 | 0.85 | 67 | CL, PG4 |
| 2 | 1079 | 0.78 | 0.80 | 94 | PEG |
| 3 | 120 | 0.60 | 0.86 | 24 | PO4 |
| 4 | 113 | 0.49 | 0.81 | 19 | PO4, MN |
| 5 | 180 | 0.48 | 0.76 | 27 | PEG |
Interfaces
1 interface between chains.
- A–B · 1974 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6PBJ · The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro… · 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 A0A0T9FW33
- Elsewhere: RCSB PDB 6PBJ · PDBe 6PBJ · UniProt A0A0T9FW33
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