MolNFT v1 · #110375 · protein
Structure of the CBM22-2 xylan-binding domain from paenibacillus barcinonensis XYN10C in complex with xylotetraose
4XUR · Endo-1,4-beta-xylanase C: “Structure of the CBM22-2 xylan-binding domain from paenibacillus barcinonensis XYN10C in complex with…”. X-ray diffraction, 2 ligands (XYP, CA), 2 pockets (best druggability 0.52). MolNFT v1 #110375 on…
- PDB
- 4XUR
- Type
- protein
- Length
- 483 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-1,4-beta-xylanase C
- EC
- 3.2.1.8
- UniProt
- O69230
- Ligands
- XYP, CA
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 161 | 7% helix, 49% strand | O69230 |
Ligands and binding sites
- XYP · beta-D-xylopyranose · sugar · 11 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 240 | 0.52 | 0.76 | 37 | empty |
| 2 | 56 | 0.32 | 0.77 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–C · 472 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 411 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XUR · Structure of the CBM22-2 xylan-binding domain from Paenibacillus barci nsis Xyn10C in… · the same entry in another collection · chain A against A, TM-score 1.00
- O69230 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase C (O69230) · a predicted model of the same protein · chain A 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 O69230
- Elsewhere: RCSB PDB 4XUR · PDBe 4XUR · UniProt O69230
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