MolNFT v1 · #146084 · protein
Apra methyltransferase 2 - gnat didomain in complex with sah
6D6Y: “Apra methyltransferase 2 - gnat didomain in complex with sah”. X-ray diffraction, 2 ligands (TMO, SAH), 5 pockets (best druggability 0.77). MolNFT v1 #146084 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D6Y
- Type
- protein
- Length
- 511 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apra methyltransferase 2
- EC
- 2.1.1.-
- UniProt
- A0A1U7N2Z8
- Ligands
- TMO, SAH
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Apra methyltransferase 2 (EC 2.1.1.-) | protein | 511 | 48% helix, 19% strand | A0A1U7N2Z8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.77 | 0.84 | 48 | SAH |
| 2 | 264 | 0.57 | 0.77 | 30 | empty |
| 3 | 118 | 0.52 | 0.81 | 32 | empty |
| 4 | 160 | 0.45 | 0.75 | 30 | empty |
| 5 | 81 | 0.31 | 0.73 | 15 | empty |
Compared structures
- 6D6Y · AprA Methyltransferase 2 - GNAT didomain in complex with SAH · 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 A0A1U7N2Z8
- Elsewhere: RCSB PDB 6D6Y · PDBe 6D6Y · UniProt A0A1U7N2Z8
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