Research workbench
High resolution crystallographic structure of the clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (XYN10B) CBM22- 1- GH10 modules complexed with xylohexaose
Analyse High resolution crystallographic structure of the clostridium thermocellum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W5F
- Type
- protein
- Length
- 1,024 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase Y
- EC
- 3.2.1.8
- UniProt
- P51584
- Ligands
- XYP, CD
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase Y (EC 3.2.1.8) | protein | 511 | 28% helix, 31% strand | P51584 |
| B | Endo-1,4-beta-xylanase Y (EC 3.2.1.8) | protein | 513 | 28% helix, 31% strand | P51584 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 6 copies · chains A, B
- CD · Cadmium ion · metal · 13 copies · chains A, B
- ACT · Acetate ion · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.82 | 0.92 | 40 | empty |
| 2 | 605 | 0.71 | 0.79 | 50 | XYP |
| 3 | 594 | 0.70 | 0.78 | 50 | XYP |
| 4 | 596 | 0.65 | 0.76 | 56 | ACT, CD |
| 5 | 494 | 0.63 | 0.76 | 51 | CD |
Interfaces
1 interface between chains.
- A–B · 913 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2W5F · High resolution crystallographic structure of the Clostridium thermocellum N-terminal… · the same entry in another collection · chain A against A, TM-score 1.00
- P51584 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase Y (P51584) · a predicted model of the same protein · chain B 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 P51584
- Elsewhere: RCSB PDB 2W5F · PDBe 2W5F · UniProt P51584
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