MolNFT v1 · #52862 · protein
The X-ray structure of the streptomyces coelicolor A3 chondroitin ac lyase in complex with chondroitin sulphate
2WDA · Putative secreted lyase: “The X-ray structure of the streptomyces coelicolor A3 chondroitin ac lyase in complex with chondroitin…”. X-ray diffraction, 3 ligands (ASG, GCD, MG), 6 pockets (best druggability 0.83). MolNFT v1 #52862 on…
- PDB
- 2WDA
- Type
- protein
- Length
- 742 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted lyase
- EC
- 4.2.2.1
- UniProt
- O86516
- Ligands
- ASG, GCD, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted lyase (EC 4.2.2.1) | protein | 742 | 33% helix, 27% strand | O86516 |
Ligands and binding sites
- ASG · 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose · ligand · chains A
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A
- FMT · Formic acid · additive · 5 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.83 | 0.84 | 63 | ASG, GCD, FMT, GOL, PEG |
| 2 | 169 | 0.46 | 0.76 | 33 | GOL, PEG |
| 3 | 67 | 0.40 | 0.80 | 17 | FMT |
| 4 | 100 | 0.36 | 0.74 | 17 | empty |
| 5 | 76 | 0.34 | 0.75 | 19 | empty |
Compared structures
- 2WDA · The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase in Complex… · 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
- Every structure of UniProt O86516
- Elsewhere: RCSB PDB 2WDA · PDBe 2WDA · UniProt O86516
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