Research workbench
Crystal structure of shikimate kinase (AQ_2177) from aquifex aeolicus VF5
Analyse Crystal structure of shikimate kinase (AQ_2177) from aquifex aeolicus VF5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PT5
- Type
- protein
- Length
- 648 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shikimate kinase
- EC
- 2.7.1.71
- UniProt
- O67925
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shikimate kinase (EC 2.7.1.71) | protein | 166 | 55% helix, 14% strand | O67925 |
| B | Shikimate kinase (EC 2.7.1.71) | protein | 168 | 56% helix, 14% strand | O67925 |
| C | Shikimate kinase (EC 2.7.1.71) | protein | 156 | 57% helix, 14% strand | O67925 |
| D | Shikimate kinase (EC 2.7.1.71) | protein | 158 | 63% helix, 14% strand | O67925 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.73 | 0.81 | 50 | empty |
| 2 | 564 | 0.73 | 0.81 | 61 | empty |
| 3 | 373 | 0.59 | 0.76 | 37 | empty |
| 4 | 253 | 0.53 | 0.76 | 29 | empty |
| 5 | 151 | 0.42 | 0.74 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–C · 603 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 469 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 454 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 378 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 2PT5 · Crystal Structure Of Shikimate Kinase (aq_2177) From Aquifex Aeolicus vf5 · the same entry in another collection · chain D against D, TM-score 1.00
- O67925 · AlphaFold monomer V2.0 prediction for shikimate kinase (O67925) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 O67925
- Elsewhere: RCSB PDB 2PT5 · PDBe 2PT5 · UniProt O67925
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