MolNFT v1 · #177446 · protein
Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S
7EIR · Chondroitin sulfate ABC endolyase: “Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S”. X-ray diffraction, 3 ligands (NG6, GCD, MG), 4 pockets (best druggability 0.53). MolNFT v1 #177446 on…
- PDB
- 7EIR
- Type
- protein
- Length
- 966 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chondroitin sulfate ABC endolyase
- EC
- 4.2.2.20
- UniProt
- P59807
- Ligands
- NG6, GCD, MG
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chondroitin sulfate ABC endolyase (EC 4.2.2.20) | protein | 966 | 27% helix, 31% strand | P59807 |
Ligands and binding sites
- NG6 · 2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose · ligand · 2 copies · chains A
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.53 | 0.77 | 40 | NG6 |
| 2 | 55 | 0.36 | 0.79 | 14 | empty |
| 3 | 72 | 0.34 | 0.75 | 19 | empty |
| 4 | 67 | 0.27 | 0.72 | 17 | empty |
Compared structures
- 7EIR · Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S · the same entry in another collection · chain A against A, TM-score 1.00
- P59807 · AlphaFold monomer V2.0 prediction for chondroitin sulfate ABC endolyase (P59807) · 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 P59807
- Elsewhere: RCSB PDB 7EIR · PDBe 7EIR · UniProt P59807
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