MolNFT v1 · #67839 · protein
T. maritima adometdc complex with S-adenosylmethionine methyl ester
3IWC · S-adenosylmethionine decarboxylase: “T. maritima adometdc complex with S-adenosylmethionine methyl ester”. X-ray diffraction, 2 ligands (PYR, SMM), 2 pockets (best druggability 0.59). MolNFT v1 #67839 on GenesisL1: 3D structure…
- PDB
- 3IWC
- Type
- protein
- Length
- 235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosylmethionine decarboxylase
- EC
- 4.1.1.50
- UniProt
- Q9WZC3
- Ligands
- PYR, SMM
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | S-adenosylmethionine decarboxylase (EC 4.1.1.50) | protein | 61 | 31% helix, 46% strand | Q9WZC3 |
| A | S-adenosylmethionine decarboxylase (EC 4.1.1.50) | protein | 58 | 28% helix, 45% strand | Q9WZC3 |
| C | S-adenosylmethionine decarboxylase (EC 4.1.1.50) | protein | 55 | 27% helix, 47% strand | Q9WZC3 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains B, A, C, D
- SMM · S-adenosylmethionine methyl ester · ligand · 2 copies · chains B, A, D, C
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 | 170 | 0.59 | 0.82 | 31 | PYR, SMM |
| 2 | 149 | 0.56 | 0.81 | 23 | PYR, SMM |
Interfaces
6 interfaces between chains.
- B–A · 2391 Ų buried · 46 hydrogen bonds · protein-protein
- D–C · 2373 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 857 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 426 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3IWC · T. maritima AdoMetDC complex with S-Adenosylmethionine methyl ester · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WZC3 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9WZC3
- Elsewhere: RCSB PDB 3IWC · PDBe 3IWC · UniProt Q9WZC3
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