MolNFT v1 · #67840 · protein
T. maritima adometdc complex with 5'-deoxy-5'-dimethyl thioadenosine
3IWD · S-adenosylmethionine decarboxylase: “T. maritima adometdc complex with 5'-deoxy-5'-dimethyl thioadenosine”. X-ray diffraction, 2 ligands (PYR, M2T), 2 pockets (best druggability 0.58). MolNFT v1 #67840 on GenesisL1: 3D structure…
- PDB
- 3IWD
- Type
- protein
- Length
- 232 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, M2T
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 47% 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, 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, D, C
- M2T · 5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine · 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 | 138 | 0.58 | 0.83 | 22 | PYR, M2T |
| 2 | 156 | 0.52 | 0.79 | 23 | PYR, M2T |
Interfaces
6 interfaces between chains.
- D–C · 2428 Ų buried · 51 hydrogen bonds · protein-protein
- B–A · 2353 Ų buried · 49 hydrogen bonds · protein-protein
- A–C · 824 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 386 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3IWD · T. maritima AdoMetDC complex with 5'-Deoxy-5'-dimethyl thioadenosine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WZC3 · AlphaFold monomer V2.0 prediction for S-adenosylmethionine decarboxylase proenzyme… · a predicted model of the same protein · chain A 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 3IWD · PDBe 3IWD · UniProt Q9WZC3
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