MolNFT v1 · #55033 · protein
Structural basis for high arginine specificity in salmonella typhimurium periplasmic binding protein STM4351.
2Y7I: “Structural basis for high arginine specificity in salmonella typhimurium periplasmic binding protein STM4351.”. X-ray diffraction, 2 ligands (ARG, ZN), 5 pockets (best druggability 0.42). MolNFT v1 #55033 on GenesisL1: 3D structure…
- PDB
- 2Y7I
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- STM4351
- UniProt
- Q8ZKA9
- Ligands
- ARG, ZN
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | STM4351 | protein | 228 | 35% helix, 23% strand | Q8ZKA9 |
| B | STM4351 | protein | 224 | 36% helix, 23% strand | Q8ZKA9 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.42 | 0.79 | 21 | ACT |
| 2 | 70 | 0.40 | 0.79 | 15 | empty |
| 3 | 75 | 0.37 | 0.77 | 17 | empty |
| 4 | 75 | 0.37 | 0.77 | 18 | ACT |
| 5 | 63 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2Y7I · Structural basis for high arginine specificity in Salmonella typhimurium periplasmic… · the same entry in another collection · chain A against A, 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 Q8ZKA9
- Elsewhere: RCSB PDB 2Y7I · PDBe 2Y7I · UniProt Q8ZKA9
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