Research workbench
Molecular insight into a new low affinity xylan binding module CBM86, from the xylanolytic gut symbiont roseburia intestinalis.
Analyse Molecular insight into a new low affinity xylan binding module CBM86, from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SGF
- Type
- protein
- Length
- 786 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-xylanase
- EC
- 3.2.1.8
- UniProt
- C7G9B5
- Ligands
- XYP, CD, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-xylanase (EC 3.2.1.8) | protein | 129 | 7% helix, 57% strand | C7G9B5 |
| B, E | Beta-xylanase (EC 3.2.1.8) | protein | 132 | 7% helix, 58% strand | C7G9B5 |
| C, F | Beta-xylanase (EC 3.2.1.8) | protein | 131 | 7% helix, 58% strand | C7G9B5 |
| D | Beta-xylanase (EC 3.2.1.8) | protein | 131 | 7% helix, 59% strand | C7G9B5 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 24 copies · chains A, B, D, C, E, F
- CD · Cadmium ion · metal · 10 copies · chains A, B, C, E, F, D
- CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.83 | 0.84 | 140 | CD |
| 2 | 201 | 0.57 | 0.80 | 40 | empty |
| 3 | 201 | 0.49 | 0.76 | 32 | empty |
| 4 | 54 | 0.39 | 0.81 | 13 | empty |
| 5 | 151 | 0.39 | 0.72 | 22 | XYP |
Interfaces
10 interfaces between chains.
- E–F · 613 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 598 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 592 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 426 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 404 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6SGF · Molecular insight into a new low affinity xylan binding module CBM86, from the… · 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 C7G9B5
- Elsewhere: RCSB PDB 6SGF · PDBe 6SGF · UniProt C7G9B5
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