MolNFT v1 · #116734 · protein
Crystal structure of the homocysteine methyltransferase mmum from escherichia COLI, apo form
5DMN · Homocysteine S-methyltransferase: “Crystal structure of the homocysteine methyltransferase mmum from escherichia COLI, apo form”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.63). MolNFT v1 #116734 on GenesisL1…
- PDB
- 5DMN
- Type
- protein
- Length
- 522 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Homocysteine S-methyltransferase
- EC
- 2.1.1.10
- UniProt
- Q47690
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Homocysteine S-methyltransferase (EC 2.1.1.10) | protein | 263 | 46% helix, 16% strand | Q47690 |
| B | Homocysteine S-methyltransferase (EC 2.1.1.10) | protein | 259 | 47% helix, 16% strand | Q47690 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.63 | 0.76 | 43 | empty |
| 2 | 301 | 0.61 | 0.79 | 42 | empty |
| 3 | 88 | 0.35 | 0.75 | 23 | empty |
| 4 | 68 | 0.28 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 626 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DMN · Crystal Structure of the Homocysteine Methyltransferase MmuM from Escherichia coli, Apo… · the same entry in another collection · chain B against B, TM-score 1.00
- Q47690 · AlphaFold monomer V2.0 prediction for homocysteine S-methyltransferase (Q47690) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5DMN · PDBe 5DMN · UniProt Q47690
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