Research workbench
Role of the biradical intermediate observed during the turnover of slac: a two-domain laccase from streptomyces coelicolor
Analyse Role of the biradical intermediate observed during the turnover of slac: a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GXF
- Type
- protein
- Length
- 837 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative copper oxidase
- UniProt
- Q9XAL8
- Ligands
- CU, O
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative copper oxidase | protein | 279 | 5% helix, 41% strand | Q9XAL8 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 12 copies · chains A, C, B
- O · Oxygen atom · ion · 3 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.85 | 0.93 | 69 | empty |
| 2 | 640 | 0.71 | 0.79 | 94 | empty |
| 3 | 127 | 0.39 | 0.74 | 16 | empty |
| 4 | 72 | 0.35 | 0.77 | 17 | empty |
| 5 | 87 | 0.34 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1899 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1893 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1892 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4GXF · Role of the biradical intermediate observed during the turnover of SLAC: A two-domain… · 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 Q9XAL8
- Elsewhere: RCSB PDB 4GXF · PDBe 4GXF · UniProt Q9XAL8
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