MolNFT v1 · #82611 · protein
Crystal structure of methyltransferase
3VSE · Putative uncharacterized protein: “Crystal structure of methyltransferase”. X-ray diffraction, 1 ligand (SAH), 15 pockets (best druggability 0.82). MolNFT v1 #82611 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VSE
- Type
- protein
- Length
- 1,554 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- Q99V16
- Ligands
- SAH
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 390 | 31% helix, 33% strand | Q99V16 |
| B | Putative uncharacterized protein | protein | 390 | 31% helix, 32% strand | Q99V16 |
| C | Putative uncharacterized protein | protein | 384 | 31% helix, 34% strand | Q99V16 |
| D | Putative uncharacterized protein | protein | 390 | 31% helix, 32% strand | Q99V16 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.82 | 0.85 | 84 | empty |
| 2 | 1103 | 0.80 | 0.82 | 122 | SAH |
| 3 | 614 | 0.78 | 0.84 | 79 | SAH |
| 4 | 726 | 0.74 | 0.80 | 79 | SAH |
| 5 | 602 | 0.71 | 0.79 | 60 | empty |
Interfaces
5 interfaces between chains.
- B–D · 869 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 638 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 114 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 59 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3VSE · Crystal structure of 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 Q99V16
- Elsewhere: RCSB PDB 3VSE · PDBe 3VSE · UniProt Q99V16
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