MolNFT v1 · #115994 · protein
Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase LYS107ALA variant regulated
5D05 · Phospho-2-dehydro-3-deoxyheptonate aldolase: “Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase LYS107ALA variant regulated”. X-ray diffraction, 5 ligands (PEP, PHE, MN), 16 pockets (best druggability…
- PDB
- 5D05
- 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, SO4, CL
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 346 | 40% helix, 18% strand | Q9K169 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 347 | 41% helix, 20% 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
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A, C
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.82 | 0.84 | 124 | PEP |
| 2 | 694 | 0.76 | 0.81 | 88 | PEP |
| 3 | 77 | 0.74 | 0.97 | 23 | empty |
| 4 | 69 | 0.73 | 0.97 | 21 | empty |
| 5 | 64 | 0.72 | 0.98 | 21 | PHE |
Interfaces
6 interfaces between chains.
- C–D · 3490 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3456 Ų buried · 67 hydrogen bonds · protein-protein
- A–C · 519 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 519 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 115 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D05 · Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Lys107Ala… · the same entry in another collection · chain D against D, 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 5D05 · PDBe 5D05 · UniProt Q9K169
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