MolNFT v1 · #114429 · protein
Crystal structure of SAM-dependent methyltransferase from geobacter sulfurreducens in complex with S-adenosyl-L-homocysteine
5BP7: “Crystal structure of SAM-dependent methyltransferase from geobacter sulfurreducens in complex with…”. X-ray diffraction, 2 ligands (SAH, CL), 9 pockets (best druggability 0.75). MolNFT v1 #114429 on GenesisL1: 3D structure, binding…
- PDB
- 5BP7
- Type
- protein
- Length
- 746 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- UniProt
- Q74AD5
- Ligands
- SAH, CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SAM-dependent methyltransferase | protein | 249 | 46% helix, 22% strand | Q74AD5 |
| B | SAM-dependent methyltransferase | protein | 248 | 46% helix, 23% strand | Q74AD5 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, C, B
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 589 | 0.75 | 0.82 | 68 | SAH |
| 2 | 554 | 0.74 | 0.81 | 59 | SAH |
| 3 | 530 | 0.71 | 0.80 | 58 | SAH |
| 4 | 135 | 0.52 | 0.81 | 28 | empty |
| 5 | 137 | 0.45 | 0.77 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 474 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 256 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 119 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5BP7 · Crystal structure of SAM-dependent methyltransferase from Geobacter sulfurreducens in… · 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 Q74AD5
- Elsewhere: RCSB PDB 5BP7 · PDBe 5BP7 · UniProt Q74AD5
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