MolNFT v1 · #171851 · protein
Crystal structure of two-domain laccase mutant R240A from streptomyces griseoflavus
6ZIP: “Crystal structure of two-domain laccase mutant R240A from streptomyces griseoflavus”. X-ray diffraction, 3 ligands (CU, OXY, PER), 20 pockets (best druggability 0.87). MolNFT v1 #171851 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6ZIP
- Type
- protein
- Length
- 3,328 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, OXY, PER
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, H, J, K | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 6% helix, 41% strand | A0A0M4FJ81 |
| C, L | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 7% helix, 42% strand | A0A0M4FJ81 |
| F, I | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% 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
- OXY · Oxygen molecule · ion · 3 copies · chains A, C, G, H, J, L
- PER · Peroxide ion · ion · chains E, F
- GOL · Glycerol · additive · 3 copies · chains B, C, E
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 | 847 | 0.87 | 0.90 | 104 | empty |
| 2 | 366 | 0.84 | 0.93 | 52 | empty |
| 3 | 366 | 0.84 | 0.93 | 46 | empty |
| 4 | 353 | 0.83 | 0.93 | 48 | empty |
| 5 | 366 | 0.83 | 0.92 | 48 | empty |
Interfaces
24 interfaces between chains.
- B–C · 1754 Ų buried · 33 hydrogen bonds · protein-protein
- G–I · 1740 Ų buried · 31 hydrogen bonds · protein-protein
- J–K · 1733 Ų buried · 35 hydrogen bonds · protein-protein
- J–L · 1728 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1726 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6ZIP · Crystal Structure of Two-Domain Laccase mutant R240A 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 6ZIP · PDBe 6ZIP · UniProt A0A0M4FJ81
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