Research workbench
Crystal structure of coclaurine N-methyltransferase (cnmt) bound to N- methylheliamine and sah
Analyse Crystal structure of coclaurine N-methyltransferase (cnmt) bound to N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKZ
- Type
- protein
- Length
- 1,346 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coclaurine N-methyltransferase
- EC
- 2.1.1.115
- UniProt
- Q948P7
- Ligands
- SAH
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coclaurine N-methyltransferase (EC 2.1.1.115) | protein | 339 | 47% helix, 17% strand | Q948P7 |
| B | Coclaurine N-methyltransferase (EC 2.1.1.115) | protein | 337 | 48% helix, 18% strand | Q948P7 |
| C | Coclaurine N-methyltransferase (EC 2.1.1.115) | protein | 337 | 47% helix, 18% strand | Q948P7 |
| D | Coclaurine N-methyltransferase (EC 2.1.1.115) | protein | 333 | 47% helix, 17% strand | Q948P7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.83 | 0.84 | 88 | empty |
| 2 | 627 | 0.77 | 0.82 | 54 | SAH |
| 3 | 621 | 0.76 | 0.82 | 54 | SAH |
| 4 | 540 | 0.75 | 0.82 | 52 | SAH |
| 5 | 603 | 0.75 | 0.82 | 58 | SAH |
Interfaces
4 interfaces between chains.
- A–D · 1160 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 286 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 6GKZ · Crystal structure of Coclaurine N-Methyltransferase (CNMT) bound to N-methylheliamine and… · the same entry in another collection · chain C against C, TM-score 1.00
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 Q948P7
- Elsewhere: RCSB PDB 6GKZ · PDBe 6GKZ · UniProt Q948P7
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