Research workbench
Crystal structure of endoglucanase from perinereis brevicirris with cellobiose
Analyse Crystal structure of endoglucanase from perinereis brevicirris with cellobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZH5
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase
- EC
- 3.2.1.4
- UniProt
- F2Z7L1
- Ligands
- BGC, NA, CA, CL
- Pockets
- 5 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoglucanase (EC 3.2.1.4) | protein | 425 | 49% helix, 7% strand | F2Z7L1 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- NA · Sodium ion · metal · 5 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.86 | 0.87 | 85 | BGC |
| 2 | 120 | 0.62 | 0.87 | 25 | NA |
| 3 | 139 | 0.58 | 0.83 | 26 | empty |
| 4 | 73 | 0.55 | 0.87 | 16 | empty |
| 5 | 54 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1018 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4ZH5 · Crystal structure of Endoglucanase from Perinereis brevicirris with Cellobiose · 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 F2Z7L1
- Elsewhere: RCSB PDB 4ZH5 · PDBe 4ZH5 · UniProt F2Z7L1
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