MolNFT v1 · #124980 · protein
Crystal structure of sorghum caffeoyl-CoA O-methyltransferase (ccoaomt)
5KVA: “Crystal structure of sorghum caffeoyl-CoA O-methyltransferase (ccoaomt)”. X-ray diffraction, 2 ligands (SAM, CA), 4 pockets (best druggability 0.68). MolNFT v1 #124980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KVA
- Type
- protein
- Length
- 455 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Caffeoyl-CoA O-methyltransferase
- UniProt
- C5Z4W3
- Ligands
- SAM, CA
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Caffeoyl-CoA O-methyltransferase | protein | 227 | 52% helix, 20% strand | C5Z4W3 |
| B | Caffeoyl-CoA O-methyltransferase | protein | 228 | 52% helix, 20% strand | C5Z4W3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- CA · Calcium 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 | 585 | 0.68 | 0.77 | 62 | SAM |
| 2 | 578 | 0.67 | 0.77 | 64 | SAM, CA |
| 3 | 82 | 0.51 | 0.84 | 17 | empty |
| 4 | 93 | 0.48 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2054 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5KVA · Crystal Structure of sorghum caffeoyl-CoA O-methyltransferase (CCoAOMT) · the same entry in another collection · chain A against A, 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 C5Z4W3
- Elsewhere: RCSB PDB 5KVA · PDBe 5KVA · UniProt C5Z4W3
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