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The study of the X-ray induced enzymatic reduction of molecular oxygen to water for laccase from steccherinum MURASHKINSKYI.THE 12-th structure of the series with total exposition time 333 min.
Analyse The study of the X-ray induced enzymatic reduction of molecular oxygen to water… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MIB
- Type
- protein
- Length
- 499 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase 2
- EC
- 1.10.3.2
- UniProt
- I1VE66
- Ligands
- NAG, CU, NA, OXY
- Pockets
- 5 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase 2 (EC 1.10.3.2) | protein | 499 | 12% helix, 37% strand | I1VE66 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CU · Copper (II) ion · metal · 4 copies · chains A
- NA · Sodium ion · metal · chains A
- OXY · Oxygen molecule · ion · 2 copies · chains A
- CIT · Citric acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.51 | 0.81 | 17 | empty |
| 2 | 169 | 0.46 | 0.75 | 28 | empty |
| 3 | 124 | 0.45 | 0.78 | 23 | empty |
| 4 | 82 | 0.35 | 0.76 | 17 | empty |
| 5 | 52 | 0.33 | 0.78 | 21 | empty |
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5MIB · The study of the X-ray induced enzymatic reduction of molecular oxygen to water for… · 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 I1VE66
- Elsewhere: RCSB PDB 5MIB · PDBe 5MIB · UniProt I1VE66
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