MolNFT v1 · #128913 · protein
Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus with 0.25 mm copper sulfate on growth medium
5O4Q: “Crystal structure of mutant M54L/M64L/M96L of two-domain laccase from streptomyces griseoflavus with 0.25 mm…”. X-ray diffraction, 3 ligands (CU, AZI, SO4), 20 pockets (best druggability 0.89). MolNFT v1 #128913 on GenesisL1: 3D…
- PDB
- 5O4Q
- Type
- protein
- Length
- 3,329 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, AZI, SO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Two-domain laccase (EC 1.10.3.2) | protein | 281 | 6% helix, 41% strand | A0A0M4FJ81 |
| B, D, E, G, H, K | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 41% strand | A0A0M4FJ81 |
| C, F, I, L | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 7% helix, 42% strand | A0A0M4FJ81 |
| J | Two-domain laccase (EC 1.10.3.2) | protein | 280 | 6% helix, 41% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- AZI · Azide ion · ion · 4 copies · chains B, C, E, F, H, I, J, K
- SO4 · Sulfate ion · ion · chains K
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, H, J
- GOL · Glycerol · additive · chains B, I
- FMT · Formic acid · additive · chains D
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 | 994 | 0.89 | 0.90 | 124 | AZI, GOL |
| 2 | 366 | 0.84 | 0.93 | 53 | empty |
| 3 | 367 | 0.83 | 0.92 | 51 | empty |
| 4 | 355 | 0.83 | 0.92 | 47 | empty |
| 5 | 344 | 0.83 | 0.93 | 42 | AZI |
Interfaces
25 interfaces between chains.
- J–L · 1912 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 1905 Ų buried · 39 hydrogen bonds · protein-protein
- J–K · 1802 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 1792 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 1791 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 5O4Q · 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 5O4Q · PDBe 5O4Q · UniProt A0A0M4FJ81
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