Research workbench
Crystal structure of E. COLI sf kinase (yihv) in complex with product sulfofructose phosphate (sfp)
Analyse Crystal structure of E. COLI sf kinase (yihv) in complex with product… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AGK
- Type
- protein
- Length
- 1,193 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
- RAH
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Sulfofructose kinase (EC 2.7.1.184) | protein | 296 | 39% helix, 26% strand | P32143 |
| A | Sulfofructose kinase (EC 2.7.1.184) | protein | 298 | 39% helix, 26% strand | P32143 |
| B | Sulfofructose kinase (EC 2.7.1.184) | protein | 299 | 38% helix, 26% strand | P32143 |
| C | Sulfofructose kinase (EC 2.7.1.184) | protein | 300 | 38% helix, 26% strand | P32143 |
Ligands and binding sites
- RAH · [(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid · ligand · 3 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.78 | 0.81 | 88 | RAH |
| 2 | 861 | 0.76 | 0.80 | 87 | RAH |
| 3 | 681 | 0.76 | 0.81 | 69 | RAH |
| 4 | 79 | 0.72 | 0.95 | 20 | empty |
| 5 | 50 | 0.65 | 0.95 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1423 Ų buried · 23 hydrogen bonds · protein-protein
- D–C · 1045 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7AGK · Crystal structure of E. coli SF kinase (YihV) in complex with product sulfofructose… · 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 D against A, TM-score 0.98
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 7AGK · PDBe 7AGK · UniProt P32143
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