MolNFT v1 · #73195 · protein
Crystal structure of the methyltransferase cobj
3NUT · Precorrin-3 methylase: “Crystal structure of the methyltransferase cobj”. X-ray diffraction, 1 ligand (SAH), 12 pockets (best druggability 0.76). MolNFT v1 #73195 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NUT
- Type
- protein
- Length
- 961 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-3 methylase
- EC
- 2.1.1.-
- UniProt
- O68097
- Ligands
- SAH
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-3 methylase (EC 2.1.1.-) | protein | 240 | 34% helix, 25% strand | O68097 |
| B | Precorrin-3 methylase (EC 2.1.1.-) | protein | 240 | 34% helix, 25% strand | O68097 |
| C | Precorrin-3 methylase (EC 2.1.1.-) | protein | 242 | 33% helix, 26% strand | O68097 |
| D | Precorrin-3 methylase (EC 2.1.1.-) | protein | 239 | 33% helix, 26% strand | O68097 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.76 | 0.81 | 65 | SAH, GOL |
| 2 | 611 | 0.75 | 0.82 | 57 | SAH |
| 3 | 622 | 0.74 | 0.81 | 69 | SAH, GOL |
| 4 | 693 | 0.73 | 0.79 | 72 | SAH, GOL |
| 5 | 125 | 0.42 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2726 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 2637 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 526 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3NUT · Crystal structure of the methyltransferase CobJ · 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 O68097
- Elsewhere: RCSB PDB 3NUT · PDBe 3NUT · UniProt O68097
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