Research workbench
Crystal structure of apo-MSNO8
Analyse Crystal structure of apo-MSNO8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4US5
- Type
- protein
- Length
- 1,323 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Luciferase-like monooxygenase
- UniProt
- W8QCH3
- Ligands
- P4G, BGC, NA, CL
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Luciferase-like monooxygenase | protein | 329 | 45% helix, 18% strand | W8QCH3 |
| B | Luciferase-like monooxygenase | protein | 331 | 44% helix, 18% strand | W8QCH3 |
| C | Luciferase-like monooxygenase | protein | 332 | 44% helix, 17% strand | W8QCH3 |
| D | Luciferase-like monooxygenase | protein | 331 | 45% helix, 17% strand | W8QCH3 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · 3 copies · chains C, D
- BGC · beta-D-glucopyranose · sugar · chains C
- NA · Sodium ion · metal · 26 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.76 | 0.96 | 28 | NA |
| 2 | 443 | 0.76 | 0.85 | 54 | empty |
| 3 | 453 | 0.74 | 0.83 | 46 | empty |
| 4 | 407 | 0.73 | 0.84 | 43 | empty |
| 5 | 430 | 0.73 | 0.83 | 50 | CL |
Interfaces
4 interfaces between chains.
- A–B · 2008 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1935 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 606 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 510 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4US5 · Crystal Structure of apo-MsnO8 · 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 W8QCH3
- Elsewhere: RCSB PDB 4US5 · PDBe 4US5 · UniProt W8QCH3
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