Research workbench
Crystal structure of sf kinase yihv from E. COLI in complex with amppnp-mg
Analyse Crystal structure of sf kinase yihv from E. COLI in complex with amppnp-mg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AGH
- Type
- protein
- Length
- 1,182 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfofructose kinase
- EC
- 2.7.1.184
- UniProt
- P32143
- Ligands
- ANP, MG
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Sulfofructose kinase (EC 2.7.1.184) | protein | 296 | 37% helix, 27% strand | P32143 |
| A | Sulfofructose kinase (EC 2.7.1.184) | protein | 295 | 37% helix, 24% strand | P32143 |
| B | Sulfofructose kinase (EC 2.7.1.184) | protein | 295 | 37% helix, 26% strand | P32143 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains C, D, A, B
- MG · Magnesium ion · metal · 3 copies · chains C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 765 | 0.76 | 0.80 | 80 | ANP |
| 2 | 1136 | 0.73 | 0.76 | 96 | ANP, MG |
| 3 | 411 | 0.69 | 0.81 | 47 | ANP, MG |
| 4 | 559 | 0.66 | 0.77 | 75 | ANP, MG |
| 5 | 267 | 0.51 | 0.75 | 41 | empty |
Interfaces
5 interfaces between chains.
- C–B · 1236 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 377 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 179 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 157 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 105 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7AGH · Crystal structure of SF kinase YihV from E. coli in complex with AMPPNP-Mg · the same entry in another collection · chain C against C, TM-score 1.00
- P32143 · AlphaFold monomer V2.0 prediction for sulfofructose kinase (P32143) · 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 P32143
- Elsewhere: RCSB PDB 7AGH · PDBe 7AGH · UniProt P32143
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