MolNFT v1 · #128872 · protein
Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus with 1 mm copper sulfate on growth medium
5O3K: “Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus with 1 mm…”. X-ray diffraction, 3 ligands (CU, O, OXY), 20 pockets (best druggability 0.88). MolNFT v1 #128872 on GenesisL1: 3D…
- PDB
- 5O3K
- Type
- protein
- Length
- 3,340 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, O, OXY
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Two-domain laccase (EC 1.10.3.2) | protein | 281 | 9% helix, 42% strand | A0A0M4FJ81 |
| B, E, H, K | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 42% strand | A0A0M4FJ81 |
| C | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | A0A0M4FJ81 |
| F, L | Two-domain laccase (EC 1.10.3.2) | protein | 276 | 5% helix, 41% strand | A0A0M4FJ81 |
| I | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 6% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 40 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- O · Oxygen atom · ion · chains A, C
- OXY · Oxygen molecule · ion · chains D, E
- GOL · Glycerol · additive · 3 copies · chains B, A, C, J, 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 | 1078 | 0.88 | 0.90 | 143 | empty |
| 2 | 451 | 0.86 | 0.93 | 68 | empty |
| 3 | 438 | 0.86 | 0.93 | 65 | empty |
| 4 | 453 | 0.85 | 0.93 | 63 | GOL |
| 5 | 390 | 0.84 | 0.92 | 56 | GOL |
Interfaces
26 interfaces between chains.
- G–I · 1868 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1842 Ų buried · 35 hydrogen bonds · protein-protein
- J–L · 1840 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 1834 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 1810 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5O3K · 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 5O3K · PDBe 5O3K · UniProt A0A0M4FJ81
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