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Crystal structure of C-terminal domain of precorrin-6Y C5,15- methyltransferase from rhodobacter capsulatus
Analyse Crystal structure of C-terminal domain of precorrin-6Y C5,15- methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NJR
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precorrin-6Y methylase
- EC
- 2.1.1.132
- UniProt
- O68099
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Precorrin-6Y methylase (EC 2.1.1.132) | protein | 184 | 34% helix, 27% strand | O68099 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains 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 | 452 | 0.65 | 0.78 | 76 | SAH |
| 2 | 489 | 0.65 | 0.77 | 73 | SAH, GOL |
| 3 | 53 | 0.32 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1515 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3NJR · Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from… · 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 O68099
- Elsewhere: RCSB PDB 3NJR · PDBe 3NJR · UniProt O68099
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