MolNFT v1 · #99444 · protein
Betaine-homocysteine S-methyltransferase from homo sapiens complexed with homocysteine
4M3P · Betaine--homocysteine S-methyltransferase 1: “Betaine-homocysteine S-methyltransferase from homo sapiens complexed with homocysteine”. X-ray diffraction, 4 ligands (HCS, SRT, ZN), 17 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 4M3P
- Type
- protein
- Length
- 1,469 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine--homocysteine S-methyltransferase 1
- EC
- 2.1.1.5
- UniProt
- Q93088
- Ligands
- HCS, SRT, ZN, K
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5) | protein | 370 | 49% helix, 11% strand | Q93088 |
| B | Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5) | protein | 373 | 49% helix, 11% strand | Q93088 |
| C | Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5) | protein | 355 | 46% helix, 11% strand | Q93088 |
| D | Betaine--homocysteine S-methyltransferase 1 (EC 2.1.1.5) | protein | 371 | 48% helix, 11% strand | Q93088 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 4 copies · chains A, B, C, D
- SRT · S,R meso-tartaric acid · ligand · 2 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- K · Potassium 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
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.82 | 0.98 | 39 | empty |
| 2 | 600 | 0.81 | 0.87 | 59 | HCS |
| 3 | 126 | 0.80 | 0.98 | 22 | empty |
| 4 | 718 | 0.79 | 0.83 | 58 | ZN, HCS |
| 5 | 575 | 0.77 | 0.83 | 48 | K, HCS |
Interfaces
6 interfaces between chains.
- C–D · 3607 Ų buried · 70 hydrogen bonds · protein-protein
- A–B · 3489 Ų buried · 72 hydrogen bonds · protein-protein
- A–D · 1231 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4M3P · Betaine-Homocysteine S-Methyltransferase from Homo sapiens complexed with Homocysteine · the same entry in another collection · chain D against D, TM-score 1.00
- Q93088 · AlphaFold monomer V2.0 prediction for betaine--homocysteine S-methyltransferase 1 (Q93088) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q93088
- Elsewhere: RCSB PDB 4M3P · PDBe 4M3P · UniProt Q93088
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