MolNFT v1 · #66923 · protein
Crystal structure of an O-methyltransferase (NCSB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L- homocysteine (sah)
3I53: “Crystal structure of an O-methyltransferase (NCSB1) from neocarzinostatin biosynthesis in complex with…”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.78). MolNFT v1 #66923 on GenesisL1: 3D structure, binding…
- PDB
- 3I53
- Type
- protein
- Length
- 628 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
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-methyltransferase (EC 2.1.1.-) | protein | 325 | 51% helix, 15% strand | Q84HC8 |
| B | O-methyltransferase (EC 2.1.1.-) | protein | 303 | 51% helix, 14% strand | Q84HC8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.78 | 0.84 | 64 | SAH |
| 2 | 409 | 0.66 | 0.79 | 41 | SAH |
| 3 | 113 | 0.48 | 0.80 | 18 | empty |
| 4 | 59 | 0.30 | 0.75 | 15 | empty |
| 5 | 73 | 0.29 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2645 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3I53 · Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in… · the same entry in another collection · chain A against A, 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 0.96
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 3I53 · PDBe 3I53 · UniProt Q84HC8
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