MolNFT v1 · #115993 · protein
Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase VAL223ALA variant regulated
5D04 · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase VAL223ALA variant regulated”. X-ray diffraction, 3 ligands (PHE, MN, CL), 8 pockets (best druggability 0.73).…
- PDB
- 5D04
- Type
- protein
- Length
- 692 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
- Q9K169
- Ligands
- PHE, MN, CL
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 346 | 41% helix, 19% strand | Q9K169 |
Ligands and binding sites
- PHE · Phenylalanine · ligand · 2 copies · chains C, D
- MN · Manganese (II) ion · metal · 2 copies · chains C, D
- CL · Chloride ion · ion · 6 copies · chains C, D
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 4 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.73 | 0.97 | 23 | empty |
| 2 | 62 | 0.72 | 0.97 | 21 | empty |
| 3 | 55 | 0.69 | 0.97 | 20 | PHE |
| 4 | 52 | 0.69 | 0.97 | 20 | PHE |
| 5 | 87 | 0.61 | 0.89 | 24 | empty |
Interfaces
1 interface between chains.
- C–D · 3454 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 5D04 · Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Val223Ala… · the same entry in another collection · chain C against C, 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 5D04 · PDBe 5D04 · UniProt Q9K169
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