Research workbench
Crystal structure of two-domain laccase mutant I170F from streptomyces griseoflavus
Analyse Crystal structure of two-domain laccase mutant I170F from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RH9
- Type
- protein
- Length
- 3,327 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-domain laccase
- EC
- 1.10.3.2
- UniProt
- A0A0M4FJ81
- Ligands
- CU, SO4, OXY
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, H, J, K | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 5% helix, 42% strand | A0A0M4FJ81 |
| C, E | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | A0A0M4FJ81 |
| F | Two-domain laccase (EC 1.10.3.2) | protein | 276 | 5% helix, 42% strand | A0A0M4FJ81 |
| G | Two-domain laccase (EC 1.10.3.2) | protein | 279 | 6% helix, 42% strand | A0A0M4FJ81 |
| I, L | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 5% helix, 43% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 48 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- SO4 · Sulfate ion · ion · chains D, E
- OXY · Oxygen molecule · ion · chains G, I
- EDO · 1,2-ethanediol · additive · 7 copies · chains C, D, G, J, L
- GOL · Glycerol · additive · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.87 | 0.89 | 109 | empty |
| 2 | 418 | 0.86 | 0.94 | 67 | empty |
| 3 | 441 | 0.86 | 0.93 | 70 | empty |
| 4 | 400 | 0.85 | 0.93 | 52 | empty |
| 5 | 367 | 0.84 | 0.93 | 49 | empty |
Interfaces
25 interfaces between chains.
- G–I · 1836 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 1805 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1802 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1794 Ų buried · 35 hydrogen bonds · protein-protein
- H–I · 1787 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6RH9 · Crystal Structure of Two-Domain Laccase mutant I170F from Streptomyces griseoflavus · 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 6RH9 · PDBe 6RH9 · UniProt A0A0M4FJ81
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