Research workbench
Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Ag, crystal of the holoenzyme soaked for 30 m in 5 mM AgNO3 at 278 K.
Analyse Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Ag… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AFA
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.193
- Source
- THERMUS THERMOPHILUS HB27
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q4H436
- Ligands
- CU, AG, OH
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.193 · 1 distinct chain · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 439 | 6% helix, 49% strand | Q4H436 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 4 copies · chains A
- AG · Silver ion · metal · 3 copies · chains A
- OH · Hydroxide ion · ion · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 8 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 6 copies · 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 | 305 | 0.61 | 0.78 | 28 | MPD, MRD |
| 2 | 166 | 0.48 | 0.77 | 31 | MRD |
| 3 | 70 | 0.34 | 0.76 | 20 | empty |
| 4 | 57 | 0.33 | 0.77 | 11 | empty |
| 5 | 61 | 0.29 | 0.74 | 17 | empty |
Compared structures
- 5AFA · Crystal structure of laccase from thermus thermophilus HB27 complexed with ag, crystal of… · 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 Q4H436
- Elsewhere: RCSB PDB 5AFA · PDBe 5AFA · UniProt Q4H436
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