Research workbench
Biochemical and structural insights into xylan utilization by the thermophilic bacteriumcaldanaerobius polysaccharolyticus
Analyse Biochemical and structural insights into xylan utilization by the thermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G68
- Type
- protein
- Length
- 1,176 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ABC transporter
- Ligands
- XYP, XYS
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | ABC transporter | protein | 392 | 48% helix, 17% strand | — |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 4 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.81 | 0.83 | 106 | empty |
| 2 | 344 | 0.78 | 0.88 | 48 | XYS, XYP |
| 3 | 352 | 0.78 | 0.88 | 53 | XYS, XYP |
| 4 | 353 | 0.76 | 0.87 | 52 | empty |
| 5 | 188 | 0.60 | 0.83 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 603 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 379 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 307 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4G68 · Biochemical and structural insights into xylan utilization by the thermophilic… · 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
- Elsewhere: RCSB PDB 4G68 · PDBe 4G68
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