Research workbench
Crystal structure of laccase from cerrena sp. RSD1
Analyse Crystal structure of laccase from cerrena sp. RSD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z1X
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- 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
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Laccase (EC 1.10.3.2) | protein | 495 | 12% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CU · Copper (II) ion · metal · 8 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.70 | 0.77 | 67 | empty |
| 2 | 129 | 0.55 | 0.82 | 21 | GOL |
| 3 | 115 | 0.53 | 0.82 | 19 | GOL |
| 4 | 212 | 0.50 | 0.76 | 32 | empty |
| 5 | 204 | 0.49 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 209 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5Z1X · Crystal Structure of Laccase from Cerrena sp. RSD1 · 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 5Z1X · PDBe 5Z1X
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