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Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose
Analyse Crystal Structure of a GH7 family cellobiohydrolase from Limnoria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAP
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Limnoria quadripunctata
- Molecule
- GH7 family protein
- EC
- 3.2.1.91
- UniProt
- D4HRL0
- Ligands
- BGC, CA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 14% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GH7 family protein (EC 3.2.1.91) | protein | 431 | 14% helix, 36% strand | D4HRL0 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
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 | 963 | 0.82 | 0.83 | 78 | BGC |
| 2 | 1118 | 0.80 | 0.82 | 87 | BGC |
| 3 | 755 | 0.74 | 0.80 | 69 | CA |
| 4 | 59 | 0.28 | 0.74 | 21 | empty |
| 5 | 51 | 0.26 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 355 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 4HAP · Crystal structure of a GH7 family cellobiohydrolase from limnoria quadripunctata in… · the same entry in another collection · chain A against A, TM-score 1.00
- D4HRL0 · AlphaFold monomer V2.0 prediction for exoglucanase GH7B (D4HRL0) · a predicted model of the same protein · chain B 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 D4HRL0
- Elsewhere: RCSB PDB 4HAP · PDBe 4HAP · UniProt D4HRL0
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