Research workbench
Small laccase from amycolatopsis sp. atcc 39116 complexed with 1-(3,4- dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-dihydroxypropane
Analyse Small laccase from amycolatopsis sp. atcc 39116 complexed with 1-(3,4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TA4
- Type
- protein
- Length
- 822 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small laccase, multi-copper oxidase
- EC
- 1.10.3.2
- Ligands
- TO2, CU
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Small laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 282 | 5% helix, 41% strand | — |
| D | Small laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 273 | 5% helix, 42% strand | — |
| E | Small laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 267 | 5% helix, 43% strand | — |
Ligands and binding sites
- TO2 · (1R,2S)-1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)propane-1,3-diol · ligand · chains F, E
- CU · Copper (II) ion · metal · 16 copies · chains F, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.86 | 0.92 | 70 | empty |
| 2 | 68 | 0.71 | 0.96 | 21 | empty |
| 3 | 67 | 0.69 | 0.96 | 20 | empty |
| 4 | 66 | 0.65 | 0.93 | 25 | empty |
| 5 | 146 | 0.51 | 0.79 | 32 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1713 Ų buried · 28 hydrogen bonds · protein-protein
- F–D · 1708 Ų buried · 30 hydrogen bonds · protein-protein
- F–E · 1682 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3TA4 · Small laccase from Amycolatopsis sp. ATCC 39116 complexed with… · the same entry in another collection · chain F against F, 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 3TA4 · PDBe 3TA4
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