Research workbench
Crystal structure of the iibsor domain of the sorbose permease from klebsiella pneumoniae solved to 1.75A resolution
Analyse Crystal structure of the iibsor domain of the sorbose permease from klebsiella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NRZ
- Type
- protein
- Length
- 652 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pts system, sorbose-specific iib component
- EC
- 2.7.1.69
- UniProt
- P37081
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pts system, sorbose-specific iib component (EC 2.7.1.69) | protein | 163 | 37% helix, 26% strand | P37081 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1065 | 0.82 | 0.83 | 103 | SO4 |
| 2 | 779 | 0.76 | 0.80 | 80 | SO4 |
| 3 | 51 | 0.35 | 0.79 | 14 | empty |
| 4 | 51 | 0.27 | 0.74 | 11 | empty |
| 5 | 50 | 0.25 | 0.73 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 804 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 749 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 274 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 271 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1NRZ · Crystal structure of the IIBSor domain of the sorbose permease from Klebsiella pneumoniae… · the same entry in another collection · chain A against A, TM-score 1.00
- P37081 · AlphaFold monomer V2.0 prediction for pts system sorbose-specific eiib component (P37081) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P37081
- Elsewhere: RCSB PDB 1NRZ · PDBe 1NRZ · UniProt P37081
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