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The structure of the catalytic and carbohydrate binding domain of endoglucanase D from clostridium cellulovorans
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
- 3NDY
- Type
- protein
- Length
- 1,804 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
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Endoglucanase D (EC 3.2.1.4) | protein | 345 | 41% helix, 12% strand | P28623 |
| E, F, G, H | Endoglucanase D (EC 3.2.1.4) | protein | 107 | 0% helix, 59% strand | P28623 |
| C | Endoglucanase D (EC 3.2.1.4) | protein | 341 | 42% helix, 13% strand | P28623 |
Ligands and binding sites
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, B, C, 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 | 1028 | 0.81 | 0.82 | 79 | BTB |
| 2 | 1034 | 0.80 | 0.82 | 83 | BTB |
| 3 | 664 | 0.74 | 0.80 | 105 | empty |
| 4 | 57 | 0.72 | 0.99 | 17 | empty |
| 5 | 576 | 0.71 | 0.80 | 93 | empty |
Interfaces
18 interfaces between chains.
- A–C · 758 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 689 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 668 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 626 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3NDY · The structure of the catalytic and carbohydrate binding domain of endoglucanase D from… · the same entry in another collection · chain H against H, TM-score 1.00
- P28623 · AlphaFold monomer V2.0 prediction for endoglucanase D (P28623) · a predicted model of the same protein · chain C 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 3NDY · PDBe 3NDY · UniProt P28623
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