Research workbench
Crystal structure of DAH7PS from neisseria meningitidis
Analyse Crystal structure of DAH7PS from neisseria meningitidis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HSN
- Type
- protein
- Length
- 1,364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
- EC
- 2.5.1.54
- UniProt
- Q9K169
- Ligands
- PEP, MN, SO4
- Pockets
- 18 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54) | protein | 341 | 41% helix, 18% strand | Q9K169 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · 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, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 16 | empty |
| 2 | 51 | 0.70 | 0.98 | 16 | empty |
| 3 | 391 | 0.69 | 0.81 | 64 | empty |
| 4 | 50 | 0.69 | 0.97 | 16 | empty |
| 5 | 260 | 0.69 | 0.84 | 40 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2913 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2810 Ų buried · 40 hydrogen bonds · protein-protein
- B–D · 559 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 554 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HSN · Crystal structure of DAH7PS from Neisseria meningitidis · 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 4HSN · PDBe 4HSN · UniProt Q9K169
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