Research workbench
Structure of an endo-xyloglucanase from cellvibrio japonicus complexed with XXXG(2F)-beta-dnp
Analyse Structure of an endo-xyloglucanase from cellvibrio japonicus complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HA9
- 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
- NFG, BGC, XYS, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellulase, putative, CEL5D (EC 3.2.1.151) | protein | 370 | 39% helix, 12% strand | B3PD52 |
Ligands and binding sites
- NFG · 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside · 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 · 5 copies · chains A, B
- GOL · Glycerol · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 458 | 0.64 | 0.77 | 56 | NFG, BGC, XYS, GOL, 1PE |
| 2 | 383 | 0.61 | 0.77 | 50 | NFG, BGC, XYS |
| 3 | 237 | 0.54 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6HA9 · Structure of an endo-Xyloglucanase from Cellvibrio japonicus complexed with… · 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 6HA9 · PDBe 6HA9 · UniProt B3PD52
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