Research workbench
Crystal structure of putative sugar binding protein (NP_459565.1) from salmonella typhimurium LT2 at 2.50 a resolution
Analyse Crystal structure of putative sugar binding protein (NP_459565.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNZ
- Type
- protein
- Length
- 1,925 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sugar binding protein
- UniProt
- Q8ZR49
- Ligands
- ETX
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Putative sugar binding protein | protein | 322 | 57% helix, 15% strand | Q8ZR49 |
| B | Putative sugar binding protein | protein | 321 | 57% helix, 14% strand | Q8ZR49 |
| C | Putative sugar binding protein | protein | 321 | 57% helix, 14% strand | Q8ZR49 |
| F | Putative sugar binding protein | protein | 317 | 55% helix, 15% strand | Q8ZR49 |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · 2 copies · chains A, C, D
- IMD · Imidazole · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.85 | 0.86 | 98 | empty |
| 2 | 848 | 0.84 | 0.86 | 61 | empty |
| 3 | 285 | 0.83 | 0.94 | 38 | empty |
| 4 | 262 | 0.83 | 0.94 | 37 | empty |
| 5 | 1170 | 0.82 | 0.83 | 85 | IMD |
Interfaces
8 interfaces between chains.
- E–F · 1826 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1658 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1632 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 478 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 457 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 66 modified (engineered).
Compared structures
- 3KNZ · Crystal structure of Putative sugar binding protein (NP_459565.1) from Salmonella… · 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 Q8ZR49
- Elsewhere: RCSB PDB 3KNZ · PDBe 3KNZ · UniProt Q8ZR49
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