Research workbench
B12-dependent radical SAM methyltransferase, MMP10 with [4FE-4S] cluster, cobalamin, and S-methyl-5'-thioadenosine bound.
Analyse B12-dependent radical SAM methyltransferase, MMP10 with [4FE-4S] cluster… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QBT
- Type
- protein
- Length
- 1,633 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyl coenzyme M reductase-arginine methyltransferase MMP10
- EC
- 2.1.1.-
- UniProt
- A0A832SFM5
- Ligands
- SF4, MTA, COB, FE, NA
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 411 | 36% helix, 16% strand | A0A832SFM5 |
| B | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 408 | 36% helix, 16% strand | A0A832SFM5 |
| C | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 404 | 36% helix, 16% strand | A0A832SFM5 |
| D | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 410 | 35% helix, 16% strand | A0A832SFM5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 4 copies · chains A, B, C, D
- COB · Co-methylcobalamin · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.80 | 0.81 | 91 | SF4, MTA, COB |
| 2 | 1113 | 0.79 | 0.81 | 92 | SF4, MTA, COB |
| 3 | 1108 | 0.79 | 0.80 | 100 | SF4, MTA, COB |
| 4 | 1189 | 0.79 | 0.80 | 104 | SF4, MTA, COB |
| 5 | 680 | 0.64 | 0.74 | 50 | empty |
Interfaces
2 interfaces between chains.
- B–D · 341 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7QBT · B12-dependent radical SAM methyltransferase, Mmp10 with [4Fe-4S] cluster, cobalamin, and… · 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 A0A832SFM5
- Elsewhere: RCSB PDB 7QBT · PDBe 7QBT · UniProt A0A832SFM5
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