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Structure of a covalent complex of endo-xyloglucanase from cellvibrio japonicus after reacting with XXXG(2F)-beta-dnp
Analyse Structure of a covalent complex of endo-xyloglucanase from cellvibrio japonicus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HAA
- Type
- protein
- Length
- 740 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulase, putative, CEL5D
- EC
- 3.2.1.151
- UniProt
- B3PD52
- Ligands
- G2F, BGC, XYS, SO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 370 | 41% helix, 14% strand | B3PD52 |
Ligands and binding sites
- G2F · 2-deoxy-2-fluoro-alpha-D-glucopyranose · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 6 copies · chains A, B
- XYS · alpha-D-xylopyranose · sugar · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 699 | 0.69 | 0.77 | 82 | G2F, BGC, XYS, PGE |
| 2 | 221 | 0.55 | 0.78 | 29 | PGE, 1PE |
| 3 | 58 | 0.32 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6HAA · Structure of a covalent complex of endo-Xyloglucanase from Cellvibrio japonicus after… · 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 B3PD52
- Elsewhere: RCSB PDB 6HAA · PDBe 6HAA · UniProt B3PD52
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