Research workbench
Zinc-bound glycoside hydrolase 61 E from thielavia terrestris
Analyse Zinc-bound glycoside hydrolase 61 E from thielavia terrestris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EII
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein GH61E
- Ligands
- NAG, ZN, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein GH61E | protein | 208 | 2% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.77 | 0.80 | 100 | ZN, GOL |
| 2 | 423 | 0.60 | 0.76 | 56 | empty |
| 3 | 278 | 0.51 | 0.75 | 38 | ZN |
| 4 | 66 | 0.40 | 0.80 | 26 | empty |
| 5 | 72 | 0.39 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 397 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 358 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 176 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 3EII · Zinc-bound glycoside hydrolase 61 E from Thielavia terrestris · 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
- Elsewhere: RCSB PDB 3EII · PDBe 3EII
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