MolNFT v1 · #66960 · protein
Crystal structure of an O-methyltransferase (NCSB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L- homocysteine (sah) and 1,4-dihydroxy-2-naphthoic acid (dhn)
3I64: “Crystal structure of an O-methyltransferase (NCSB1) from neocarzinostatin biosynthesis in complex with…”. X-ray diffraction, 2 ligands (SAH, DNA), 6 pockets (best druggability 0.80). MolNFT v1 #66960 on GenesisL1: 3D structure…
- PDB
- 3I64
- Type
- protein
- Length
- 656 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q84HC8
- Ligands
- SAH, DNA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | O-methyltransferase (EC 2.1.1.-) | protein | 328 | 52% helix, 16% strand | Q84HC8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- DNA · 1,4-dihydroxy-2-naphthoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.80 | 0.84 | 90 | SAH, DNA |
| 2 | 210 | 0.73 | 0.89 | 35 | SAH |
| 3 | 344 | 0.72 | 0.84 | 39 | DNA |
| 4 | 102 | 0.37 | 0.75 | 24 | empty |
| 5 | 62 | 0.30 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 2709 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3I64 · Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in… · the same entry in another collection · chain B against B, TM-score 1.00
- Q84HC8 · AlphaFold monomer V2.0 prediction for 2,7-dihydroxy-5-methyl-1-naphthoate… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q84HC8
- Elsewhere: RCSB PDB 3I64 · PDBe 3I64 · UniProt Q84HC8
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