Research workbench
Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4- glucanase from ruminal metagenomic library, in the native form
Analyse Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4- glucanase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W84
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xyloglucan-specific endo-beta-1,4-glucanase
- EC
- 3.2.1.151
- UniProt
- D2K7Z0
- Ligands
- MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xyloglucan-specific endo-beta-1,4-glucanase (EC 3.2.1.151) | protein | 340 | 42% helix, 14% strand | D2K7Z0 |
| B | Xyloglucan-specific endo-beta-1,4-glucanase (EC 3.2.1.151) | protein | 339 | 42% helix, 14% strand | D2K7Z0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · 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 | 388 | 0.66 | 0.80 | 47 | MG |
| 2 | 266 | 0.54 | 0.76 | 36 | TRS |
| 3 | 254 | 0.53 | 0.76 | 33 | TRS |
Interfaces
1 interface between chains.
- A–B · 352 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 4W84 · Crystal structure of XEG5A, a GH5 xyloglucan-specific endo-beta-1,4-glucanase from… · 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 D2K7Z0
- Elsewhere: RCSB PDB 4W84 · PDBe 4W84 · UniProt D2K7Z0
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