Research workbench
Human adometdc with 5'-[(4-AMINOOXYBUTYL)METHYLAMINO]-5'DEOXY-8- ethyladenosine
Analyse Human adometdc with 5'-[(4-AMINOOXYBUTYL)METHYLAMINO]-5'DEOXY-8- ethyladenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZ6
- Type
- protein
- Length
- 293 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase beta chain; S-adenosylmethionine decarboxylase alpha…
- EC
- 4.1.1.50
- UniProt
- P17707
- Ligands
- PYR, PUT, M8E
- Pockets
- 1 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 56 | 25% helix, 39% strand | P17707 |
| A | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 237 | 23% helix, 42% strand | P17707 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains B, A
- PUT · 1,4-diaminobutane · ligand · chains B, A
- M8E · 5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.65 | 0.86 | 23 | PYR, M8E |
Interfaces
1 interface between chains.
- B–A · 3151 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3DZ6 · Human AdoMetDC with 5'-[(4-aminooxybutyl)methylamino]-5'deoxy-8-ethyladenosine · the same entry in another collection · chain B against B, TM-score 1.00
- P17707 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P17707
- Elsewhere: RCSB PDB 3DZ6 · PDBe 3DZ6 · UniProt P17707
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