Research workbench
Crystal structure of helicobactor pylori shikimate kinase in complex with NSC162535
Analyse Crystal structure of helicobactor pylori shikimate kinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N2E
- Type
- protein
- Length
- 464 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- P56073
- Ligands
- OSA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 168 | 62% helix, 14% strand | P56073 |
| B | Shikimate kinase (EC 2.7.1.71) | protein | 162 | 62% helix, 15% strand | P56073 |
| C | Shikimate kinase (EC 2.7.1.71) | protein | 134 | 49% helix, 18% strand | P56073 |
Ligands and binding sites
- OSA · 7-amino-4-hydroxy-3-[(E)-(5-hydroxy-7-sulfonaphthalen-2-yl)diazenyl]naphthalene-2-sulfonic acid · ligand · 2 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.73 | 0.79 | 57 | OSA, TLA |
| 2 | 439 | 0.69 | 0.80 | 42 | OSA, TLA |
| 3 | 101 | 0.52 | 0.83 | 14 | empty |
| 4 | 61 | 0.30 | 0.75 | 13 | empty |
| 5 | 67 | 0.30 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 593 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 412 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3N2E · Crystal structure of Helicobactor pylori shikimate kinase in complex with NSC162535 · the same entry in another collection · chain A against A, TM-score 1.00
- P56073 · AlphaFold monomer V2.0 prediction for shikimate kinase (P56073) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P56073
- Elsewhere: RCSB PDB 3N2E · PDBe 3N2E · UniProt P56073
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