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X-ray crystal structure of the endo-beta-N- acetylglucosaminidase from arthrobacter protophormiae E173Q mutant reveals a tim barrel catalytic domain and two ancillary domains
Analyse X-ray crystal structure of the endo-beta-N- acetylglucosaminidase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VTF
- Type
- protein
- Length
- 1,232 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endo-beta-N-acetylglucosaminidase
- EC
- 3.2.1.96
- UniProt
- Q9ZB22
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 616 | 19% helix, 32% strand | Q9ZB22 |
| B | Endo-beta-N-acetylglucosaminidase (EC 3.2.1.96) | protein | 616 | 19% helix, 32% strand | Q9ZB22 |
Ligands and binding sites
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.71 | 0.81 | 45 | empty |
| 2 | 307 | 0.69 | 0.83 | 28 | empty |
| 3 | 739 | 0.67 | 0.75 | 64 | empty |
| 4 | 205 | 0.63 | 0.83 | 26 | B3P |
| 5 | 264 | 0.61 | 0.80 | 31 | B3P |
Interfaces
1 interface between chains.
- A–B · 187 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2VTF · X-ray crystal structure of the Endo-beta-N-acetylglucosaminidase from Arthrobacter… · 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 Q9ZB22
- Elsewhere: RCSB PDB 2VTF · PDBe 2VTF · UniProt Q9ZB22
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