MolNFT v1 · #144812 · protein
Crystal structure analysis of laphzm
6C5B · Methyltransferase: “Crystal structure analysis of laphzm”. X-ray diffraction, 2 ligands (SAH, NA), 6 pockets (best druggability 0.80). MolNFT v1 #144812 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6C5B
- Type
- protein
- Length
- 664 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- A0A172J1V3
- Ligands
- SAH, NA
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyltransferase | protein | 332 | 52% helix, 15% strand | A0A172J1V3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 298 | 0.80 | 0.91 | 55 | SAH, FMT |
| 2 | 287 | 0.80 | 0.91 | 57 | SAH, FMT |
| 3 | 721 | 0.69 | 0.76 | 82 | P33 |
| 4 | 271 | 0.57 | 0.78 | 32 | empty |
| 5 | 109 | 0.44 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3551 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6C5B · Crystal Structure Analysis of LaPhzM · 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 A0A172J1V3
- Elsewhere: RCSB PDB 6C5B · PDBe 6C5B · UniProt A0A172J1V3
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