Research workbench
Apo structure of cellobiohydrolase 1 (CEL7A) from heterobasidion annosum
Analyse Apo structure of cellobiohydrolase 1 (CEL7A) from heterobasidion annosum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YG1
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellulose 1,4-beta-cellobiosidase
- EC
- 3.2.1.-
- Ligands
- NAG, MG
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellulose 1,4-beta-cellobiosidase (EC 3.2.1.-) | protein | 440 | 14% helix, 34% strand | — |
| B | Cellulose 1,4-beta-cellobiosidase (EC 3.2.1.-) | protein | 426 | 15% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.79 | 0.81 | 82 | empty |
| 2 | 780 | 0.74 | 0.79 | 61 | empty |
| 3 | 337 | 0.61 | 0.78 | 58 | empty |
| 4 | 183 | 0.55 | 0.80 | 38 | empty |
| 5 | 169 | 0.52 | 0.79 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 831 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 2YG1 · Apo structure of cellobiohydrolase 1 (CEL7A) from heterobasidion annosum · 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 2YG1 · PDBe 2YG1
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