Research workbench
Closed liganded crystal structure of xylose binding protein from Escherichia coli
Analyse Closed liganded crystal structure of xylose binding protein from Escherichia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MA0
- Type
- protein
- Length
- 925 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli
- Molecule
- D-xylose-binding periplasmic protein
- UniProt
- P37387
- Ligands
- XYP
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-xylose-binding periplasmic protein | protein | 313 | 44% helix, 21% strand | P37387 |
| B, C | D-xylose-binding periplasmic protein | protein | 306 | 44% helix, 21% strand | P37387 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1194 | 0.77 | 0.79 | 123 | empty |
| 2 | 188 | 0.56 | 0.80 | 27 | empty |
| 3 | 185 | 0.52 | 0.78 | 26 | empty |
| 4 | 60 | 0.42 | 0.82 | 17 | empty |
| 5 | 57 | 0.29 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 959 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 596 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3MA0 · Closed liganded crystal structure of xylose binding protein from escherichia COLI · the same entry in another collection · chain A against A, TM-score 1.00
- P37387 · AlphaFold monomer V2.0 prediction for D-xylose-binding periplasmic protein (P37387) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P37387
- Elsewhere: RCSB PDB 3MA0 · PDBe 3MA0 · UniProt P37387
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