MolNFT v1 · #143512 · protein
Crystal structure of ps I-cgsb C78S in complex with I-neocarratetraose
6B1V · Iota-carrageenan sulfatase: “Crystal structure of ps I-cgsb C78S in complex with I-neocarratetraose”. X-ray diffraction, 3 ligands (G4S, DGS, CA), 10 pockets (best druggability 0.80). MolNFT v1 #143512 on GenesisL1: 3D structure…
- PDB
- 6B1V
- Type
- protein
- Length
- 1,356 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iota-carrageenan sulfatase
- Ligands
- G4S, DGS, CA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Iota-carrageenan sulfatase | protein | 452 | 36% helix, 16% strand | — |
Ligands and binding sites
- G4S · 4-O-sulfo-beta-D-galactopyranose · ligand · 10 copies · chains A, B, C
- DGS · 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose · ligand · 10 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.80 | 0.84 | 75 | empty |
| 2 | 360 | 0.66 | 0.80 | 51 | G4S, DGS |
| 3 | 475 | 0.65 | 0.77 | 62 | G4S, DGS |
| 4 | 226 | 0.63 | 0.82 | 42 | G4S |
| 5 | 260 | 0.57 | 0.78 | 46 | EDO |
Interfaces
3 interfaces between chains.
- B–C · 949 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 944 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 866 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6B1V · Crystal structure of Ps i-CgsB C78S in complex with i-neocarratetraose · 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 6B1V · PDBe 6B1V
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