Research workbench
Crystal structure of the pyrrolizidine alkaloid N-oxygenase from zonocerus variegatus in complex with FAD and NADP+
Analyse Crystal structure of the pyrrolizidine alkaloid N-oxygenase from zonocerus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NMX
- Type
- protein
- Length
- 1,628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin-containing monooxygenase
- EC
- 1.-.-.-
- UniProt
- L0N8S9
- Ligands
- FAD, NAP, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Flavin-containing monooxygenase (EC 1.-.-.-) | protein | 406 | 31% helix, 25% strand | L0N8S9 |
| B | Flavin-containing monooxygenase (EC 1.-.-.-) | protein | 407 | 30% helix, 25% strand | L0N8S9 |
| D | Flavin-containing monooxygenase (EC 1.-.-.-) | protein | 409 | 30% helix, 25% strand | L0N8S9 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.87 | 0.88 | 111 | FAD, NAP |
| 2 | 1032 | 0.84 | 0.84 | 98 | FAD, NAP |
| 3 | 1130 | 0.83 | 0.83 | 107 | FAD, NAP |
| 4 | 1065 | 0.83 | 0.83 | 97 | FAD, NAP |
| 5 | 1006 | 0.75 | 0.78 | 60 | empty |
Interfaces
4 interfaces between chains.
- A–B · 550 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 228 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 173 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5NMX · Crystal Structure of the pyrrolizidine alkaloid N-oxygenase from Zonocerus variegatus in… · the same entry in another collection · chain D against D, 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 L0N8S9
- Elsewhere: RCSB PDB 5NMX · PDBe 5NMX · UniProt L0N8S9
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