Research workbench
Crystal structure of steccherinum ochraceum laccase obtained by multi- crystals composite data collection technique (10% dose)
Analyse Crystal structure of steccherinum ochraceum laccase obtained by multi- crystals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T6W
- Type
- protein
- Length
- 1,485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- Ligands
- NAG, CU, SO4, OXY
- Pockets
- 17 · best druggability 0.91
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Laccase (EC 1.10.3.2) | protein | 495 | 11% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B, C
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
- OXY · Oxygen molecule · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.91 | 0.93 | 146 | SO4, GOL |
| 2 | 101 | 0.65 | 0.89 | 22 | SO4 |
| 3 | 67 | 0.50 | 0.85 | 14 | GOL |
| 4 | 185 | 0.49 | 0.76 | 35 | empty |
| 5 | 163 | 0.48 | 0.77 | 31 | GOL |
Interfaces
3 interfaces between chains.
- A–B · 832 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 827 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 3T6W · Crystal Structure of Steccherinum ochraceum Laccase obtained by multi-crystals composite… · 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
- Elsewhere: RCSB PDB 3T6W · PDBe 3T6W
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