MolNFT v1 · #38027 · protein
Cytoplasmic protein STM3548 from salmonella typhimurium
2GK3 · Putative cytoplasmic protein: “Cytoplasmic protein STM3548 from salmonella typhimurium”. X-ray diffraction, 12 pockets (best druggability 0.77). MolNFT v1 #38027 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GK3
- Type
- protein
- Length
- 1,478 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cytoplasmic protein
- UniProt
- Q8ZLF9
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Putative cytoplasmic protein | protein | 246 | 26% helix, 35% strand | Q8ZLF9 |
| E | Putative cytoplasmic protein | protein | 248 | 26% helix, 34% strand | Q8ZLF9 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, C, D, B, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.77 | 0.96 | 21 | empty |
| 2 | 743 | 0.76 | 0.81 | 67 | GOL |
| 3 | 117 | 0.76 | 0.96 | 21 | empty |
| 4 | 620 | 0.75 | 0.81 | 53 | GOL |
| 5 | 723 | 0.74 | 0.80 | 75 | GOL |
Interfaces
15 interfaces between chains.
- C–E · 1335 Ų buried · 24 hydrogen bonds · protein-protein
- B–F · 1327 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1322 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 925 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 915 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 modified (engineered).
Compared structures
- 2GK3 · Cytoplasmic Protein STM3548 from Salmonella typhimurium · the same entry in another collection · chain E against E, TM-score 1.00
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 Q8ZLF9
- Elsewhere: RCSB PDB 2GK3 · PDBe 2GK3 · UniProt Q8ZLF9
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