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The X-ray structure of the streptomyces coelicolor A3 chondroitin ac lyase Y253A mutant
Analyse The X-ray structure of the streptomyces coelicolor A3 chondroitin ac lyase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X03
- Type
- protein
- Length
- 1,485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted lyase
- EC
- 4.2.2.1
- UniProt
- O86516
- Ligands
- MG
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted lyase (EC 4.2.2.1) | protein | 742 | 34% helix, 27% strand | O86516 |
| B | Putative secreted lyase (EC 4.2.2.1) | protein | 743 | 33% helix, 27% strand | O86516 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.80 | 0.82 | 111 | empty |
| 2 | 1001 | 0.73 | 0.76 | 77 | empty |
| 3 | 864 | 0.72 | 0.77 | 77 | empty |
| 4 | 100 | 0.44 | 0.78 | 17 | empty |
| 5 | 126 | 0.41 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 691 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2X03 · The X-ray structure of the Streptomyces coelicolor A3 Chondroitin AC Lyase Y253A mutant · 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 2X03 · PDBe 2X03 · UniProt O86516
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