MolNFT v1 · #148676 · protein
Crystal structure of two-domain laccase mutant H165A from streptomyces griseoflavus with high copper ions occupancy
6FDJ: “Crystal structure of two-domain laccase mutant H165A from streptomyces griseoflavus with high copper ions…”. X-ray diffraction, 2 ligands (CU, OXY), 20 pockets (best druggability 0.88). MolNFT v1 #148676 on GenesisL1: 3D structure…
- PDB
- 6FDJ
- Type
- protein
- Length
- 3,321 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
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, G | Two-domain laccase (EC 1.10.3.2) | protein | 278 | 5% helix, 41% strand | A0A0M4FJ81 |
| C, F | Two-domain laccase (EC 1.10.3.2) | protein | 275 | 7% helix, 41% strand | A0A0M4FJ81 |
| E, H | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 5% helix, 43% strand | A0A0M4FJ81 |
| I, L | Two-domain laccase (EC 1.10.3.2) | protein | 276 | 7% helix, 42% strand | A0A0M4FJ81 |
| J | Two-domain laccase (EC 1.10.3.2) | protein | 277 | 6% helix, 42% strand | A0A0M4FJ81 |
| K | Two-domain laccase (EC 1.10.3.2) | protein | 276 | 6% helix, 41% 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 · 6 copies · chains A, B, C, D, F, G, I, J, K, L
- GOL · Glycerol · additive · 12 copies · chains A, B, D, E, F, G, H, I, J, K, L
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 | 1114 | 0.88 | 0.89 | 153 | empty |
| 2 | 513 | 0.86 | 0.93 | 71 | GOL |
| 3 | 473 | 0.86 | 0.93 | 71 | GOL |
| 4 | 688 | 0.86 | 0.90 | 97 | GOL |
| 5 | 412 | 0.85 | 0.93 | 62 | GOL |
Interfaces
25 interfaces between chains.
- J–K · 1768 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1742 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1738 Ų buried · 35 hydrogen bonds · protein-protein
- G–H · 1732 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1723 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6FDJ · Crystal Structure of Two-Domain Laccase mutant H165A 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 6FDJ · PDBe 6FDJ · UniProt A0A0M4FJ81
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