Research workbench
Crystal structure of human soluble catechol O-methyltransferase in complex with 3,5-dinitrocatechol and sinefungin
Analyse Crystal structure of human soluble catechol O-methyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I3D
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol O-methyltransferase
- EC
- 2.1.1.6
- UniProt
- P21964
- Ligands
- DNC, SFG, MG
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 214 | 49% helix, 23% strand | P21964 |
| B | Catechol O-methyltransferase (EC 2.1.1.6) | protein | 218 | 45% helix, 22% strand | P21964 |
Ligands and binding sites
- DNC · 3,5-dinitrocatechol · ligand · 2 copies · chains A, B
- SFG · Sinefungin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.60 | 0.85 | 31 | DNC, MG, SFG |
| 2 | 142 | 0.58 | 0.83 | 31 | DNC, SFG |
| 3 | 273 | 0.54 | 0.75 | 31 | empty |
| 4 | 55 | 0.29 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 412 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6I3D · Crystal structure of Human soluble catechol O-methyltransferase in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
- P21964 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase (P21964) · 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 P21964
- Elsewhere: RCSB PDB 6I3D · PDBe 6I3D · UniProt P21964
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