Research workbench
Crystal structure of S213G variant DAH7PS from neisseria meningitidis
Analyse Crystal structure of S213G variant 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
- 4HSO
- Type
- protein
- Length
- 1,380 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
- TYR, PEP, MN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54) | protein | 345 | 40% helix, 19% strand | Q9K169 |
| B | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54) | protein | 343 | 40% helix, 19% strand | Q9K169 |
| C, D | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (EC 2.5.1.54) | protein | 346 | 39% helix, 20% strand | Q9K169 |
Ligands and binding sites
- TYR · Tyrosine · ligand · 4 copies · chains A, B, C, D
- PEP · Phosphoenolpyruvate · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.81 | 0.85 | 113 | TYR |
| 2 | 267 | 0.81 | 0.93 | 55 | TYR |
| 3 | 57 | 0.72 | 0.98 | 17 | empty |
| 4 | 58 | 0.71 | 0.98 | 18 | empty |
| 5 | 55 | 0.70 | 0.98 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3384 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 3189 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 562 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 557 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 62 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4HSO · Crystal structure of S213G variant DAH7PS from Neisseria meningitidis · the same entry in another collection · chain B against B, 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 4HSO · PDBe 4HSO · UniProt Q9K169
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