Research workbench
Crystal structure of laccase from thermus thermophilus HB27 complexed with hg, crystal of the apoenzyme soaked for 5 min. in 5 mm HGCL2 at 278 K.
Analyse Crystal structure of laccase from thermus thermophilus HB27 complexed with hg… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XVB
- Type
- protein
- Length
- 439 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laccase
- EC
- 1.10.3.2
- UniProt
- Q72HW2
- Ligands
- HG
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Laccase (EC 1.10.3.2) | protein | 439 | 6% helix, 48% strand | Q72HW2 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 5 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains A
- MRD · (4R)-2-methylpentane-2,4-diol · 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 | 297 | 0.61 | 0.79 | 28 | MPD |
| 2 | 136 | 0.44 | 0.76 | 26 | MRD, MPD |
| 3 | 74 | 0.38 | 0.78 | 21 | empty |
| 4 | 65 | 0.37 | 0.78 | 11 | empty |
| 5 | 63 | 0.30 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 2XVB · Crystal structure of Laccase from Thermus thermophilus HB27 complexed with Hg, 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 Q72HW2
- Elsewhere: RCSB PDB 2XVB · PDBe 2XVB · UniProt Q72HW2
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