MolNFT v1 · #163360 · protein
Crystal structure of two-domain laccase from streptomyces griseoflavus produced at 0.25 mm copper sulfate in growth medium
6S0O: “Crystal structure of two-domain laccase from streptomyces griseoflavus produced at 0.25 mm copper sulfate in…”. X-ray diffraction, 3 ligands (PEO, CU, SO4), 15 pockets (best druggability 0.87). MolNFT v1 #163360 on GenesisL1: 3D…
- PDB
- 6S0O
- Type
- protein
- Length
- 1,666 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-domain laccase
- EC
- 1.10.3.2
- UniProt
- A0A0M4FJ81
- Ligands
- PEO, CU, SO4
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 41% strand | A0A0M4FJ81 |
| B | Two-domain laccase (EC 1.10.3.2) | protein | 280 | 7% helix, 42% strand | A0A0M4FJ81 |
| C | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 5% helix, 42% strand | A0A0M4FJ81 |
| F | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 5% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- PEO · Hydrogen peroxide · ligand · 2 copies · chains A, B, C
- CU · Copper (II) ion · metal · 24 copies · chains A, C, B, D, F, E
- SO4 · Sulfate ion · ion · 2 copies · chains D, F, E
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.87 | 0.89 | 98 | empty |
| 2 | 413 | 0.85 | 0.93 | 66 | GOL |
| 3 | 423 | 0.85 | 0.93 | 73 | empty |
| 4 | 243 | 0.75 | 0.89 | 31 | empty |
| 5 | 60 | 0.71 | 0.97 | 19 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1833 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1796 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1788 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1780 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1756 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 6S0O · Crystal Structure of Two-Domain Laccase from Streptomyces griseoflavus produced at 0.25… · 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 A0A0M4FJ81
- Elsewhere: RCSB PDB 6S0O · PDBe 6S0O · UniProt A0A0M4FJ81
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