MolNFT v1 · #172867 · protein
Crystal structure of E. COLI sf kinase (yihv) in complex with product sulfofructose phosphate (sfp)
7AGK · Sulfofructose kinase: “Crystal structure of E. COLI sf kinase (yihv) in complex with product sulfofructose phosphate (sfp)”. X-ray diffraction, 1 ligand (RAH), 11 pockets (best druggability 0.78). MolNFT v1 #172867 on GenesisL1: 3D…
- 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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