MolNFT v1 · #35084 · protein
Crystal structure of cbil in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic vitamin B12 biosynthesis
2E0N · Precorrin-2 C20-methyltransferase: “Crystal structure of cbil in complex with S-adenosylhomocysteine, a methyltransferase involved in anaerobic…”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 2E0N
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-2 C20-methyltransferase
- EC
- 2.1.1.130
- UniProt
- Q8KFD9
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precorrin-2 C20-methyltransferase (EC 2.1.1.130) | protein | 229 | 34% helix, 26% strand | Q8KFD9 |
| B | Precorrin-2 C20-methyltransferase (EC 2.1.1.130) | protein | 238 | 30% helix, 21% strand | Q8KFD9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.81 | 0.87 | 56 | SAH |
| 2 | 485 | 0.76 | 0.84 | 51 | SAH |
| 3 | 68 | 0.32 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1929 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2E0N · Crystal structure of CbiL in complex with S-adenosylhomocysteine, a methyltransferase… · the same entry in another collection · chain B against B, 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 Q8KFD9
- Elsewhere: RCSB PDB 2E0N · PDBe 2E0N · UniProt Q8KFD9
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