Research workbench
Human S-adenosylmethionine decarboxylase with covalently bound pyruvoyl group and complexed with 4-amidinoindan-1-one-2'- amidinohydrazone
Analyse Human S-adenosylmethionine decarboxylase with covalently bound pyruvoyl group… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I7M
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- 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, CG
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 57 | 21% helix, 30% strand | P17707 |
| A, C | S-adenosylmethionine decarboxylase alpha chain (EC 4.1.1.50) | protein | 248 | 23% helix, 39% strand | P17707 |
| D | S-adenosylmethionine decarboxylase beta chain (EC 4.1.1.50) | protein | 55 | 22% helix, 33% strand | P17707 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains B, A, D, C
- PUT · 1,4-diaminobutane · ligand · 2 copies · chains B, A, D, C
- CG · 4-amidinoindan-1-one-2'-amidinohydrazone · ligand · 2 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.66 | 0.88 | 29 | PYR, CG |
| 2 | 109 | 0.55 | 0.84 | 26 | PYR, CG |
| 3 | 187 | 0.48 | 0.76 | 29 | empty |
| 4 | 136 | 0.42 | 0.75 | 19 | empty |
| 5 | 129 | 0.39 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- B–A · 3102 Ų buried · 55 hydrogen bonds · protein-protein
- D–C · 3069 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 936 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 1I7M · Human S-adenosylmethionine decarboxylase with covalently bound pyruvoyl group and… · the same entry in another collection · chain C against C, 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 1I7M · PDBe 1I7M · UniProt P17707
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