Research workbench
Human adometdc with 5'-[(CARBOXAMIDOMETHYL)METHYLAMINO]-5'-deoxy-8- methyladenosine
Analyse Human adometdc with 5'-[(CARBOXAMIDOMETHYL)METHYLAMINO]-5'-deoxy-8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZ7
- Type
- protein
- Length
- 303 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, O8M
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 61 | 23% helix, 36% strand | P17707 |
| A | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 242 | 22% helix, 40% strand | P17707 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains B, A
- PUT · 1,4-diaminobutane · ligand · chains B, A
- O8M · 2-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]acetamide · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets 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 | 26 | PYR, O8M |
| 2 | 54 | 0.31 | 0.76 | 13 | empty |
| 3 | 79 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 3217 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3DZ7 · Human AdoMetDC with 5'-[(carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine · 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 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 P17707
- Elsewhere: RCSB PDB 3DZ7 · PDBe 3DZ7 · UniProt P17707
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