Research workbench
Crystal structure of pseudomonas stutzeri endoglucanase CEL5A in complex with cellobiose
Analyse Crystal structure of pseudomonas stutzeri endoglucanase CEL5A 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
- 6R2J
- Type
- protein
- Length
- 1,310 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ENDOGLUCANASE(ENDO-1,4-beta-GLUCANASE)PROTEIN
- UniProt
- A4VME5
- Ligands
- BGC
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ENDOGLUCANASE(ENDO-1,4-beta-GLUCANASE)PROTEIN | protein | 326 | 33% helix, 17% strand | A4VME5 |
| B | ENDOGLUCANASE(ENDO-1,4-beta-GLUCANASE)PROTEIN | protein | 330 | 32% helix, 17% strand | A4VME5 |
| C | ENDOGLUCANASE(ENDO-1,4-beta-GLUCANASE)PROTEIN | protein | 325 | 32% helix, 17% strand | A4VME5 |
| D | ENDOGLUCANASE(ENDO-1,4-beta-GLUCANASE)PROTEIN | protein | 329 | 33% helix, 17% strand | A4VME5 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, D
- TRS · 2-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
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.83 | 0.85 | 93 | empty |
| 2 | 185 | 0.63 | 0.84 | 31 | empty |
| 3 | 331 | 0.57 | 0.76 | 54 | empty |
| 4 | 249 | 0.56 | 0.78 | 26 | empty |
| 5 | 236 | 0.54 | 0.77 | 42 | BGC, TRS |
Interfaces
5 interfaces between chains.
- C–D · 570 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 273 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 245 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6R2J · Crystal Structure of Pseudomonas stutzeri endoglucanase Cel5A in complex 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 A4VME5
- Elsewhere: RCSB PDB 6R2J · PDBe 6R2J · UniProt A4VME5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.