Research workbench
Structure of a putative xyloglucanase from the cellulolytic bacteria streptomyces sp. sirexaa-E
Analyse Structure of a putative xyloglucanase from the cellulolytic bacteria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JWZ
- Type
- protein
- Length
- 1,447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose-binding family II
- UniProt
- G2NK78
- Ligands
- CA
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulose-binding family II | protein | 724 | 3% helix, 38% strand | G2NK78 |
| B | Cellulose-binding family II | protein | 723 | 2% helix, 39% strand | G2NK78 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.84 | 0.93 | 36 | empty |
| 2 | 351 | 0.84 | 0.93 | 38 | empty |
| 3 | 1055 | 0.77 | 0.79 | 104 | empty |
| 4 | 254 | 0.72 | 0.87 | 48 | CA |
| 5 | 256 | 0.70 | 0.85 | 54 | CA |
Interfaces
1 interface between chains.
- A–B · 734 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5JWZ · Structure of a Putative Xyloglucanase from the Cellulolytic Bacteria Streptomyces sp.… · 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 G2NK78
- Elsewhere: RCSB PDB 5JWZ · PDBe 5JWZ · UniProt G2NK78
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