Research workbench
Crystal structure of ps I-cgsb C78S in complex with K-carrapentaose
Analyse Crystal structure of ps I-cgsb C78S in complex with K-carrapentaose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0K
- Type
- protein
- Length
- 1,353 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iota-carrageenan sulfatase
- Ligands
- G4S, 9RN, ARG, CA, CL
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Iota-carrageenan sulfatase | protein | 451 | 35% helix, 17% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 8 copies · chains A, B, C
- 9RN · 3,6-anhydro-alpha-D-galactopyranose · ligand · 6 copies · chains A, B, C
- ARG · Arginine · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.79 | 0.85 | 65 | CL |
| 2 | 347 | 0.62 | 0.78 | 47 | empty |
| 3 | 376 | 0.62 | 0.78 | 53 | G4S, 9RN, EDO |
| 4 | 211 | 0.55 | 0.79 | 28 | empty |
| 5 | 183 | 0.54 | 0.79 | 38 | G4S, 9RN, EDO |
Interfaces
3 interfaces between chains.
- A–B · 1008 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 967 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 950 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6B0K · Crystal structure of Ps i-CgsB C78S in complex with k-carrapentaose · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6B0K · PDBe 6B0K
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