Research workbench
Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase PHE211ALA variant
Analyse Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D09
- Type
- protein
- Length
- 1,330 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, TMO, MN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 334 | 41% helix, 17% strand | Q9K169 |
| C | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 333 | 42% helix, 17% strand | Q9K169 |
| D | Phospho-2-dehydro-3-deoxyheptonate aldolase (EC 2.5.1.54) | protein | 329 | 42% helix, 17% strand | Q9K169 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- TMO · trimethylamine oxide · ligand · chains A
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.79 | 0.81 | 123 | EDO |
| 2 | 974 | 0.79 | 0.81 | 117 | empty |
| 3 | 95 | 0.75 | 0.96 | 23 | empty |
| 4 | 177 | 0.69 | 0.87 | 29 | empty |
| 5 | 72 | 0.65 | 0.92 | 18 | PEP |
Interfaces
6 interfaces between chains.
- A–B · 1591 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1458 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 572 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 567 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 62 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5D09 · Neisseria meningitidis 3 deoxy-D-arabino-heptulosonate 7-phosphate synthase Phe211Ala… · 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 5D09 · PDBe 5D09 · UniProt Q9K169
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