MolNFT v1 · #185123 · protein
Crystal structure of two-domain laccase mutant M199A from streptomyces griseoflavus
7PFR: “Crystal structure of two-domain laccase mutant M199A from streptomyces griseoflavus”. X-ray diffraction, 2 ligands (CU, NA), 18 pockets (best druggability 0.84). MolNFT v1 #185123 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7PFR
- Type
- protein
- Length
- 1,668 residues
- Chains
- 6
- 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, NA
- Pockets
- 18 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 41% strand | A0A0M4FJ81 |
| C | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | A0A0M4FJ81 |
| D | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 5% helix, 42% strand | A0A0M4FJ81 |
| F | Two-domain laccase (EC 1.10.3.2) | protein | 279 | 6% helix, 42% strand | A0A0M4FJ81 |
Ligands and binding sites
- CU · Copper (II) ion · metal · 24 copies · chains A, C, B, D, F, E
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 376 | 0.84 | 0.93 | 53 | NA |
| 2 | 387 | 0.84 | 0.93 | 61 | NA |
| 3 | 494 | 0.82 | 0.89 | 73 | empty |
| 4 | 620 | 0.81 | 0.86 | 90 | empty |
| 5 | 165 | 0.73 | 0.91 | 40 | empty |
Interfaces
12 interfaces between chains.
- D–E · 1830 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 1813 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1811 Ų buried · 32 hydrogen bonds · protein-protein
- D–F · 1789 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1781 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 7PFR · Crystal Structure of Two-Domain Laccase mutant M199A from Streptomyces griseoflavus · 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 7PFR · PDBe 7PFR · UniProt A0A0M4FJ81
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