MolNFT v1 · #62761 · protein
Human adometdc E178Q mutant with no putrescine bound
3EP5 · S-adenosylmethionine decarboxylase beta chain: “Human adometdc E178Q mutant with no putrescine bound”. X-ray diffraction, 2 ligands (PYR, URE), 3 pockets (best druggability 0.72). MolNFT v1 #62761 on GenesisL1: 3D structure, binding…
- PDB
- 3EP5
- Type
- protein
- Length
- 296 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, URE
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 57 | 21% helix, 39% strand | P17707 |
| A | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 239 | 21% helix, 40% strand | P17707 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · chains B, A
- URE · Urea · ligand · chains B, A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.72 | 0.99 | 15 | URE |
| 2 | 172 | 0.65 | 0.85 | 27 | PYR, TRS |
| 3 | 73 | 0.37 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 3210 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3EP5 · Human AdoMetDC E178Q mutant with no putrescine bound · 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 3EP5 · PDBe 3EP5 · UniProt P17707
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