MolNFT v1 · #148629 · protein
Crystal structure of two-domain laccase mutant H165F from streptomyces griseoflavus with high copper ions occupancy
6FC7: “Crystal structure of two-domain laccase mutant H165F from streptomyces griseoflavus with high copper ions…”. X-ray diffraction, 3 ligands (CU, PER, OXY), 20 pockets (best druggability 0.89). MolNFT v1 #148629 on GenesisL1: 3D…
- PDB
- 6FC7
- Type
- protein
- Length
- 3,351 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, PER, OXY
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G, I, J | Two-domain laccase (EC 1.10.3.2) | protein | 281 | 6% helix, 42% strand | A0A0M4FJ81 |
| B | Two-domain laccase (EC 1.10.3.2) | protein | 281 | 6% helix, 41% strand | A0A0M4FJ81 |
| C, F | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 5% helix, 42% strand | A0A0M4FJ81 |
| D, E, H | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 41% strand | A0A0M4FJ81 |
| K | Two-domain laccase (EC 1.10.3.2) | protein | 282 | 7% helix, 41% strand | A0A0M4FJ81 |
| L | Two-domain laccase (EC 1.10.3.2) | protein | 276 | 7% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 48 copies · chains A, C, B, D, F, E, G, I, H, J, L, K
- PER · Peroxide ion · ion · 6 copies · chains B, C, D, F, E, G, H, J, K, L
- OXY · Oxygen molecule · ion · 2 copies · chains D, E, J, L
- GOL · Glycerol · additive · chains B
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 | 977 | 0.89 | 0.90 | 105 | empty |
| 2 | 406 | 0.85 | 0.93 | 65 | empty |
| 3 | 381 | 0.84 | 0.93 | 64 | empty |
| 4 | 383 | 0.84 | 0.93 | 61 | empty |
| 5 | 405 | 0.84 | 0.92 | 62 | empty |
Interfaces
26 interfaces between chains.
- A–C · 1923 Ų buried · 43 hydrogen bonds · protein-protein
- H–I · 1900 Ų buried · 39 hydrogen bonds · protein-protein
- J–K · 1897 Ų buried · 38 hydrogen bonds · protein-protein
- J–L · 1890 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1865 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 6FC7 · Crystal Structure of Two-Domain Laccase mutant H165F from Streptomyces griseoflavus with… · 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 6FC7 · PDBe 6FC7 · UniProt A0A0M4FJ81
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