MolNFT v1 · #55129 · protein
X-ray induced reduction of laccase from thermus thermophilus HB27 (87.5-100.0 percent dose)
2YAR: “X-ray induced reduction of laccase from thermus thermophilus HB27 (87.5-100.0 percent dose)”. X-ray diffraction, 2 ligands (CU, OH), 5 pockets (best druggability 0.62). MolNFT v1 #55129 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2YAR
- 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
- CU, OH
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 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 | Q72HW2 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 3 copies · chains A
- OH · Hydroxide ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 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 | 299 | 0.62 | 0.79 | 27 | MPD, MRD |
| 2 | 160 | 0.47 | 0.76 | 26 | MRD |
| 3 | 86 | 0.38 | 0.77 | 21 | empty |
| 4 | 59 | 0.34 | 0.78 | 12 | empty |
| 5 | 76 | 0.32 | 0.74 | 17 | empty |
Compared structures
- 2YAR · X-ray induced reduction of laccase from Thermus thermophilus HB27 (87. 5-100.0 percent… · 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 2YAR · PDBe 2YAR · UniProt Q72HW2
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