MolNFT v1 · #116395 · protein
Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with pep
5DCB · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase regulated and complexed with pep”. X-ray diffraction, 5 ligands (PEP, PHE, MN), 13 pockets (best druggability…
- PDB
- 5DCB
- Type
- protein
- Length
- 1,385 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, CL, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 346 | 41% helix, 18% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 348 | 41% helix, 18% strand | Q9K169 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 345 | 41% 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
- CL · Chloride ion · ion · 3 copies · chains A, B, D
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, D
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.75 | 0.84 | 77 | PEP |
| 2 | 304 | 0.73 | 0.86 | 56 | PEP |
| 3 | 67 | 0.73 | 0.98 | 20 | empty |
| 4 | 63 | 0.72 | 0.98 | 19 | PHE |
| 5 | 68 | 0.72 | 0.97 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3382 Ų buried · 64 hydrogen bonds · protein-protein
- C–D · 3346 Ų buried · 61 hydrogen bonds · protein-protein
- B–D · 511 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 508 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
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 5DCB · PDBe 5DCB · UniProt Q9K169
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