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Crystal structure of the complex of the kappa-carrageenase from pseudoalteromonas carrageenovora with an oligotetrasaccharide of kappa-carrageenan
Analyse Crystal structure of the complex of the kappa-carrageenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OCQ
- Type
- protein
- Length
- 550 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kappa-carrageenase
- EC
- 3.2.1.83
- UniProt
- P43478
- Ligands
- 9RN, G4S
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kappa-carrageenase (EC 3.2.1.83) | protein | 271 | 5% helix, 53% strand | P43478 |
| B | Kappa-carrageenase (EC 3.2.1.83) | protein | 279 | 5% helix, 53% strand | P43478 |
Ligands and binding sites
- 9RN · 3,6-anhydro-alpha-D-galactopyranose · ligand · 4 copies · chains A, B
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 4 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.71 | 0.80 | 44 | G4S, 9RN |
| 2 | 534 | 0.70 | 0.79 | 41 | G4S, 9RN |
Compared structures
- 5OCQ · Crystal structure of the complex of the kappa-carrageenase from Pseudoalteromonas… · the same entry in another collection · chain A against A, TM-score 1.00
- P43478 · AlphaFold monomer V2.0 prediction for kappa-carrageenase (P43478) · 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 P43478
- Elsewhere: RCSB PDB 5OCQ · PDBe 5OCQ · UniProt P43478
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