MolNFT v1 · #12860 · protein
Iota-carrageenase complexed to iota-carrageenan fragments
1KTW: “Iota-carrageenase complexed to iota-carrageenan fragments”. X-ray diffraction, 5 ligands (G4S, DGS, CA), 7 pockets (best druggability 0.71). MolNFT v1 #12860 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KTW
- Type
- protein
- Length
- 914 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iota-carrageenase
- EC
- 3.2.1.157
- Ligands
- G4S, DGS, CA, NA, CL
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Iota-carrageenase (EC 3.2.1.157) | protein | 457 | 14% helix, 40% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 3 copies · chains A
- DGS · 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose · ligand · 3 copies · chains A
- CA · Calcium ion · metal · 10 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.71 | 0.76 | 67 | G4S, DGS, CL |
| 2 | 349 | 0.61 | 0.78 | 49 | empty |
| 3 | 192 | 0.57 | 0.80 | 22 | empty |
| 4 | 386 | 0.57 | 0.74 | 51 | CL |
| 5 | 61 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 377 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1KTW · Iota-carrageenase complexed to iota-carrageenan fragments · 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 1KTW · PDBe 1KTW
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