Research workbench
Small laccase from streptomyces viridosporus T7A; alternate crystal form complexed with acetovanillone.
Analyse Small laccase from streptomyces viridosporus T7A; alternate crystal form… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TBC
- Type
- protein
- Length
- 834 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small laccase, two-domain laccase, multi-copper oxidase
- EC
- 1.10.3.2
- Ligands
- I75, TAM, CU, PO4, OXY
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small laccase, two-domain laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 279 | 6% helix, 41% strand | — |
| B | Small laccase, two-domain laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 278 | 6% helix, 42% strand | — |
| C | Small laccase, two-domain laccase, multi-copper oxidase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | — |
Ligands and binding sites
- I75 · 1-(4-hydroxy-3-methoxyphenyl)ethanone · ligand · chains C
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains C
- CU · Copper (II) ion · metal · 12 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 7 copies · chains A, C, B
- OXY · Oxygen molecule · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.84 | 0.93 | 57 | empty |
| 2 | 57 | 0.69 | 0.97 | 20 | PO4 |
| 3 | 52 | 0.68 | 0.97 | 19 | PO4 |
| 4 | 222 | 0.63 | 0.82 | 44 | PO4 |
| 5 | 184 | 0.55 | 0.80 | 32 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1843 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1804 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1779 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 3TBC · Small laccase from Streptomyces viridosporus T7A; alternate crystal form complexed with… · 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 3TBC · PDBe 3TBC
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