MolNFT v1 · #171956 · protein
Phage SAM lyase in complex with S-methyl-5'-thioadenosine
6ZM9 · Chains: a: “Phage SAM lyase in complex with S-methyl-5'-thioadenosine”. X-ray diffraction, 4 ligands (PRO, MTA, NA), 1 pocket (best druggability 0.51). MolNFT v1 #171956 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZM9
- Type
- protein
- Length
- 129 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chains: a
- Ligands
- PRO, MTA, NA, PO4
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chains: a | protein | 129 | 26% helix, 40% strand | — |
Ligands and binding sites
- PRO · Proline · ligand · chains A
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.51 | 0.82 | 21 | PRO, MTA |
Compared structures
- 6ZM9 · Phage SAM lyase in complex with S-methyl-5'-thioadenosine · 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
- Elsewhere: RCSB PDB 6ZM9 · PDBe 6ZM9
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