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Crystal structure of fi-cmcase from aspergillus aculeatus F-50 in complex with cellobiose
Analyse Crystal structure of fi-cmcase from aspergillus aculeatus F-50 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GM5
- Type
- protein
- Length
- 1,530 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase-1
- EC
- 3.2.1.4
- UniProt
- P22669
- Ligands
- BGC, SO4
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F | Endoglucanase-1 (EC 3.2.1.4) | protein | 218 | 9% helix, 55% strand | P22669 |
| B, G | Endoglucanase-1 (EC 3.2.1.4) | protein | 219 | 9% helix, 56% strand | P22669 |
| E | Endoglucanase-1 (EC 3.2.1.4) | protein | 220 | 10% helix, 55% strand | P22669 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 8 copies · chains A, D, F, G
- SO4 · Sulfate ion · ion · 9 copies · chains A, C, B, D, E, G, F
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.83 | 0.83 | 129 | BGC |
| 2 | 400 | 0.71 | 0.82 | 49 | BGC |
| 3 | 887 | 0.70 | 0.76 | 93 | empty |
| 4 | 541 | 0.69 | 0.78 | 59 | BGC |
| 5 | 504 | 0.68 | 0.79 | 53 | BGC |
Interfaces
10 interfaces between chains.
- D–E · 836 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 799 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 741 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 313 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 5GM5 · Crystal structure of FI-CMCase from Aspergillus aculeatus F-50 in complex with cellobiose · the same entry in another collection · chain G against G, TM-score 1.00
- P22669 · AlphaFold monomer V2.0 prediction for endoglucanase-1 (P22669) · a predicted model of the same protein · 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 P22669
- Elsewhere: RCSB PDB 5GM5 · PDBe 5GM5 · UniProt P22669
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