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Structure of a paenibacillus polymyxa xyloglucanase from glycoside hydrolase family 44
Analyse Structure of a paenibacillus polymyxa xyloglucanase from glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YKK
- Type
- protein
- Length
- 512 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CEL44C
- EC
- 3.2.1.4, 3.2.1.151
- UniProt
- Q1A2D0
- Ligands
- CA, SO4, CL
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CEL44C (EC 3.2.1.4, 3.2.1.151) | protein | 512 | 31% helix, 26% strand | Q1A2D0 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- CL · Chloride ion · ion · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.63 | 0.78 | 48 | BTB |
| 2 | 142 | 0.49 | 0.79 | 20 | empty |
| 3 | 70 | 0.30 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2YKK · Structure of a Paenibacillus Polymyxa Xyloglucanase from Glycoside Hydrolase Family 44 · 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 Q1A2D0
- Elsewhere: RCSB PDB 2YKK · PDBe 2YKK · UniProt Q1A2D0
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