Research workbench
Crystal structure of selenomethionine-incorporated nicotine oxidoreductase from pseudomonas putida
Analyse Crystal structure of selenomethionine-incorporated nicotine oxidoreductase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TTK
- Type
- protein
- Length
- 1,734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amine oxidase
- UniProt
- F8G0P2
- Ligands
- FAD
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amine oxidase | protein | 432 | 37% helix, 25% strand | F8G0P2 |
| C, D | Amine oxidase | protein | 435 | 35% helix, 25% strand | F8G0P2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.86 | 0.87 | 95 | FAD |
| 2 | 1074 | 0.86 | 0.86 | 94 | FAD |
| 3 | 1070 | 0.85 | 0.86 | 96 | FAD |
| 4 | 1158 | 0.85 | 0.85 | 100 | FAD |
| 5 | 889 | 0.78 | 0.81 | 81 | empty |
Interfaces
5 interfaces between chains.
- B–D · 1656 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 733 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 697 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 335 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 79 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 5TTK · Crystal Structure of Selenomethionine-incorporated Nicotine Oxidoreductase from… · 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 F8G0P2
- Elsewhere: RCSB PDB 5TTK · PDBe 5TTK · UniProt F8G0P2
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