Research workbench
Crystal structure of the sixth cohesin from acetivibrio cellulolyticus' scaffoldin B in complex with CEL5 dockerin S15I, I16N mutant
Analyse Crystal structure of the sixth cohesin from acetivibrio cellulolyticus'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NRK
- Type
- protein
- Length
- 421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglucanase; DOCCEL5: type I dockerin repeat domain from a. cellulolyticus family 5…
- EC
- 3.2.1.4
- UniProt
- Q9RPL0
- Ligands
- CA, SCN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Endoglucanase (EC 3.2.1.4) | protein | 143 | 3% helix, 57% strand | Q9RPL0 |
| B | DOCCEL5: type I dockerin repeat domain from a. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant | protein | 68 | 40% helix, 0% strand | — |
| D | DOCCEL5: type I dockerin repeat domain from a. cellulolyticus family 5 endoglucanase WP_010249057 S15I, I16N mutant | protein | 67 | 40% helix, 0% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains B, D
- SCN · Thiocyanate ion · ion · 3 copies · chains B, D, C
- GOL · Glycerol · additive · 2 copies · chains A, B, D
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 | 215 | 0.55 | 0.78 | 32 | SCN |
| 2 | 145 | 0.50 | 0.79 | 32 | empty |
| 3 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 791 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 779 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 471 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 244 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 186 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5NRK · Crystal structure of the sixth cohesin from Acetivibrio cellulolyticus' scaffoldin B in… · 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 Q9RPL0
- Elsewhere: RCSB PDB 5NRK · PDBe 5NRK · UniProt Q9RPL0
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