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X-ray crystal structure of the catalytic domain of thermobifida fusca endoglucanase CEL5A (E5)
Analyse X-ray crystal structure of the catalytic domain of thermobifida fusca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CKS
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase E-5
- EC
- 3.2.1.4
- UniProt
- Q01786
- Ligands
- BEN, ZN, NA
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglucanase E-5 (EC 3.2.1.4) | protein | 305 | 44% helix, 17% strand | Q01786 |
| B | Endoglucanase E-5 (EC 3.2.1.4) | protein | 306 | 42% helix, 19% strand | Q01786 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 8 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.58 | 0.75 | 57 | ZN, NA |
| 2 | 146 | 0.48 | 0.78 | 24 | ZN |
| 3 | 82 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 142 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2CKS · X-ray crystal structure of the catalytic domain of thermobifida fusca endoglucanase CEL5A… · 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
- Every structure of UniProt Q01786
- Elsewhere: RCSB PDB 2CKS · PDBe 2CKS · UniProt Q01786
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