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The structure of the catalytic and carbohydrate binding domain of endoglucanase D from clostridium cellulovorans bound to cellotriose
Analyse The structure of the catalytic and carbohydrate binding domain of endoglucanase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NDZ
- Type
- protein
- Length
- 1,808 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase D
- EC
- 3.2.1.4
- UniProt
- P28623
- Ligands
- BGC
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endoglucanase D (EC 3.2.1.4) | protein | 345 | 41% helix, 13% strand | P28623 |
| E, F, G, H | Endoglucanase D (EC 3.2.1.4) | protein | 107 | 0% helix, 61% strand | P28623 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 18 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.81 | 0.82 | 80 | BGC |
| 2 | 1099 | 0.80 | 0.82 | 84 | BGC |
| 3 | 1083 | 0.75 | 0.78 | 123 | empty |
| 4 | 1166 | 0.75 | 0.78 | 130 | empty |
| 5 | 50 | 0.70 | 0.98 | 16 | empty |
Interfaces
18 interfaces between chains.
- B–D · 752 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 750 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 691 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 683 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 630 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3NDZ · The structure of the catalytic and carbohydrate binding domain of endoglucanase D from… · the same entry in another collection · chain G against G, TM-score 1.00
- P28623 · AlphaFold monomer V2.0 prediction for endoglucanase D (P28623) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P28623
- Elsewhere: RCSB PDB 3NDZ · PDBe 3NDZ · UniProt P28623
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