MolNFT v1 · #116733 · protein
Crystal structure of the homocysteine methyltransferase mmum from escherichia COLI, metallated form
5DMM · Homocysteine S-methyltransferase: “Crystal structure of the homocysteine methyltransferase mmum from escherichia COLI, metallated form”. X-ray diffraction, 2 ligands (HCS, ZN), 1 pocket (best druggability 0.73). MolNFT v1 #116733 on…
- PDB
- 5DMM
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homocysteine S-methyltransferase
- EC
- 2.1.1.10
- UniProt
- Q47690
- Ligands
- HCS, ZN
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homocysteine S-methyltransferase (EC 2.1.1.10) | protein | 288 | 49% helix, 15% strand | Q47690 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- BME · Beta-mercaptoethanol · additive · 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 | 291 | 0.73 | 0.86 | 29 | BME, HCS |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5DMM · Crystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47690 · AlphaFold monomer V2.0 prediction for homocysteine S-methyltransferase (Q47690) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q47690
- Elsewhere: RCSB PDB 5DMM · PDBe 5DMM · UniProt Q47690
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