MolNFT v1 · #128905 · protein
Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus dialyzed against solution containing 0.25 mm copper sulfate
5O4I: “Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus dialyzed…”. X-ray diffraction, 2 ligands (CU, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #128905 on GenesisL1: 3D structure…
- PDB
- 5O4I
- Type
- protein
- Length
- 3,336 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Two-domain laccase
- EC
- 1.10.3.2
- UniProt
- A0A0M4FJ81
- Ligands
- CU, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, G, K | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 7% helix, 42% strand | A0A0M4FJ81 |
| B | Two-domain laccase (EC 1.10.3.2) | protein | 281 | 8% helix, 41% strand | A0A0M4FJ81 |
| C, F, H | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | A0A0M4FJ81 |
| I | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 6% helix, 42% strand | A0A0M4FJ81 |
| J | Two-domain laccase (EC 1.10.3.2) | protein | 279 | 6% helix, 42% strand | A0A0M4FJ81 |
| L | Two-domain laccase (EC 1.10.3.2) | protein | 280 | 6% helix, 41% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 36 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, D, F, G, H, J
- GOL · Glycerol · additive · 43 copies · chains A, B, C, D, F, E, G, H, I, J, L, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.86 | 0.94 | 67 | GOL |
| 2 | 450 | 0.86 | 0.93 | 69 | GOL |
| 3 | 431 | 0.86 | 0.94 | 72 | GOL |
| 4 | 878 | 0.84 | 0.86 | 118 | GOL |
| 5 | 200 | 0.77 | 0.92 | 41 | empty |
Interfaces
26 interfaces between chains.
- A–B · 1864 Ų buried · 38 hydrogen bonds · protein-protein
- K–L · 1829 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1777 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1740 Ų buried · 33 hydrogen bonds · protein-protein
- D–E · 1730 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5O4I · Crystal Structure of mutant M54L/M64L/M96L of Two-Domain Laccase from Streptomyces… · 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 A0A0M4FJ81
- Elsewhere: RCSB PDB 5O4I · PDBe 5O4I · UniProt A0A0M4FJ81
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