Research workbench
Structure-based redesign of cofactor binding in putrescine oxidase: wild type bound to putrescine
Analyse Structure-based redesign of cofactor binding in putrescine oxidase: wild type… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YG4
- Type
- protein
- Length
- 899 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine oxidase
- EC
- 1.4.3.10
- UniProt
- B0F9F6
- Ligands
- FAD, 4HA, SO4
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putrescine oxidase (EC 1.4.3.10) | protein | 449 | 42% helix, 24% strand | B0F9F6 |
| B | Putrescine oxidase (EC 1.4.3.10) | protein | 450 | 41% helix, 24% strand | B0F9F6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 4HA · 4-hydroxybutan-1-aminium · ligand · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.87 | 0.96 | 64 | FAD, 4HA |
| 2 | 347 | 0.87 | 0.96 | 66 | 4HA, FAD |
| 3 | 70 | 0.71 | 0.97 | 21 | empty |
| 4 | 227 | 0.59 | 0.80 | 23 | SO4 |
| 5 | 212 | 0.57 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2092 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2YG4 · Structure-based redesign of cofactor binding in Putrescine Oxidase: wild type bound to… · 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 B0F9F6
- Elsewhere: RCSB PDB 2YG4 · PDBe 2YG4 · UniProt B0F9F6
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