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Crystal structure of two-domain laccase mutant R240H from streptomyces griseoflavus
Analyse Crystal structure of two-domain laccase mutant R240H from streptomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZIJ
- Type
- protein
- Length
- 1,663 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
- CU, MG, OXY
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 5% helix, 42% strand | A0A0M4FJ81 |
| B, D, E | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 5% 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 | 7% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, C, B, D, F, E
- MG · Magnesium ion · metal · 3 copies · chains C, A, B, D, E, F
- OXY · Oxygen molecule · ion · 6 copies · chains A, C, B, D, F, E
- GOL · Glycerol · additive · 5 copies · chains A, C, E, F
- 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
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.88 | 0.90 | 103 | empty |
| 2 | 378 | 0.85 | 0.93 | 49 | MG |
| 3 | 370 | 0.84 | 0.93 | 46 | MG |
| 4 | 282 | 0.76 | 0.89 | 40 | empty |
| 5 | 54 | 0.71 | 0.98 | 19 | empty |
Interfaces
13 interfaces between chains.
- D–F · 1783 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1766 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1760 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1751 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 1751 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6ZIJ · Crystal Structure of Two-Domain Laccase mutant R240H 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 6ZIJ · PDBe 6ZIJ · UniProt A0A0M4FJ81
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