Research workbench
Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from paenibacillus barcinonensis XYN10C
Analyse Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from paenibacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XUP
- Type
- protein
- Length
- 1,615 residues
- Chains
- 6
- 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
- CA
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 330 | 3% helix, 48% strand | O69230 |
| B | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 321 | 3% helix, 49% strand | O69230 |
| C | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 159 | 0% helix, 49% strand | O69230 |
| D | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 321 | 3% helix, 50% strand | O69230 |
| E | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 159 | 0% helix, 49% strand | O69230 |
| F | Endo-1,4-beta-xylanase C (EC 3.2.1.8) | protein | 325 | 3% helix, 49% strand | O69230 |
Ligands and binding sites
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.86 | 0.88 | 139 | empty |
| 2 | 988 | 0.85 | 0.86 | 126 | empty |
| 3 | 379 | 0.75 | 0.86 | 53 | empty |
| 4 | 703 | 0.71 | 0.78 | 49 | empty |
| 5 | 139 | 0.60 | 0.85 | 32 | GOL |
Interfaces
11 interfaces between chains.
- A–D · 1499 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1133 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 765 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 751 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 725 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4XUP · Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barci nsis… · the same entry in another collection · chain F against F, 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 E against A, TM-score 0.98
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 4XUP · PDBe 4XUP · UniProt O69230
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.