MolNFT v1 · #115981 · protein
Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase GLU98ALA variant regulated
5CZS · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase GLU98ALA variant regulated”. X-ray diffraction, 3 ligands (PEP, PHE, MN), 14 pockets (best druggability 0.74).…
- PDB
- 5CZS
- Type
- protein
- Length
- 1,378 residues
- Chains
- 4
- 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
- Q9K169
- Ligands
- PEP, PHE, MN
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 344 | 40% helix, 19% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 345 | 39% helix, 19% strand | Q9K169 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 345 | 40% helix, 19% strand | Q9K169 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- PHE · Phenylalanine · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.74 | 0.83 | 72 | PEP |
| 2 | 423 | 0.73 | 0.84 | 64 | PEP, EDO |
| 3 | 308 | 0.72 | 0.85 | 56 | empty |
| 4 | 69 | 0.71 | 0.96 | 22 | PHE |
| 5 | 235 | 0.71 | 0.87 | 39 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3280 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3141 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 529 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 515 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CZS · Neisseria meningitidis 3 dexy-D-arabino-heptulosonate 7-phosphate synthase Glu98Ala… · 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 Q9K169
- Elsewhere: RCSB PDB 5CZS · PDBe 5CZS · UniProt Q9K169
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