Research workbench
Crystal structure of ps I-cgsb in complex with K-I-K-neocarrahexaose
Analyse Crystal structure of ps I-cgsb in complex with K-I-K-neocarrahexaose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B0J
- Type
- protein
- Length
- 1,354 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iota-carrageenan sulfatase
- Ligands
- G4S, 9RN, DGS, ARG, CA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Iota-carrageenan sulfatase | protein | 452 | 35% helix, 17% strand | — |
| B, C | Iota-carrageenan sulfatase | protein | 451 | 35% helix, 17% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 12 copies · chains A, B, C
- 9RN · 3,6-anhydro-alpha-D-galactopyranose · ligand · 7 copies · chains A, B, C
- DGS · 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose · ligand · 5 copies · chains A, B, C
- ARG · Arginine · ligand · 2 copies · chains A, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.80 | 0.85 | 79 | empty |
| 2 | 223 | 0.61 | 0.82 | 29 | empty |
| 3 | 170 | 0.54 | 0.80 | 25 | empty |
| 4 | 193 | 0.54 | 0.79 | 22 | empty |
| 5 | 95 | 0.45 | 0.80 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 969 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 927 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6B0J · Crystal structure of Ps i-CgsB in complex with k-i-k-neocarrahexaose · 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
- Elsewhere: RCSB PDB 6B0J · PDBe 6B0J
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