Research workbench
Human adometdc with 5'-deoxy-5'-[(N-DIMETHYL)AMINO]-8-methyl-adenosine
Analyse Human adometdc with 5'-deoxy-5'-[(N-DIMETHYL)AMINO]-8-methyl-adenosine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H0W
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase proenzyme
- EC
- 4.1.1.50
- UniProt
- P17707
- Ligands
- PUT, N8M, PYR
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 61 | 23% helix, 36% strand | P17707 |
| A | S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) | protein | 238 | 24% helix, 40% strand | P17707 |
Ligands and binding sites
- PUT · 1,4-diaminobutane · ligand · chains B, A
- N8M · 5'-deoxy-5'-(dimethylamino)-8-methyladenosine · ligand · chains B, A
- PYR · Pyruvic acid · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.66 | 0.86 | 27 | N8M, PYR |
| 2 | 88 | 0.61 | 0.89 | 23 | PUT |
Interfaces
1 interface between chains.
- B–A · 3202 Ų buried · 55 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3H0W · Human AdoMetDC with 5'-Deoxy-5'-[(N-dimethyl)amino]-8-methyl-adenosine · 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 3H0W · PDBe 3H0W · UniProt P17707
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