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
- 7QBU
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- 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
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 418 | 35% helix, 17% strand | A0A832SFM5 |
| B | Methyl coenzyme M reductase-arginine methyltransferase MMP10 (EC 2.1.1.-) | protein | 407 | 35% helix, 17% strand | A0A832SFM5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
- COB · Co-methylcobalamin · ligand · 2 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 988 | 0.81 | 0.82 | 92 | SF4, MTA, COB, PEG |
| 2 | 1153 | 0.79 | 0.81 | 99 | SF4, MTA, COB, PEG |
| 3 | 1006 | 0.71 | 0.75 | 58 | empty |
| 4 | 457 | 0.58 | 0.74 | 43 | empty |
| 5 | 50 | 0.33 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 227 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7QBU · 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 7QBU · PDBe 7QBU · UniProt A0A832SFM5
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