MolNFT v1 · #21100 · protein
Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (dahps) from thermotoga maritima complexed with CD2+, pep and E4P
1RZM · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (dahps) from thermotoga maritima…”. X-ray diffraction, 3 ligands (PEP, E4P, CD), 3 pockets (best druggability…
- PDB
- 1RZM
- Type
- protein
- Length
- 676 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
- Q9WYH8
- Ligands
- PEP, E4P, CD
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 338 | 35% helix, 21% strand | Q9WYH8 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- E4P · Erythose-4-phosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.78 | 0.99 | 18 | empty |
| 2 | 165 | 0.63 | 0.85 | 31 | PEP, E4P |
| 3 | 166 | 0.59 | 0.83 | 27 | PEP, E4P |
Interfaces
1 interface between chains.
- A–B · 1582 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1RZM · Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHPS) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WYH8 · AlphaFold monomer V2.0 prediction for phospho-2-dehydro-3-deoxyheptonate aldolase (Q9WYH8) · a predicted model of the same protein · chain A against A, TM-score 0.82
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 Q9WYH8
- Elsewhere: RCSB PDB 1RZM · PDBe 1RZM · UniProt Q9WYH8
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