MolNFT v1 · #26556 · protein
Crystal structure of human T-protein of glycine cleavage system
1WSV · Aminomethyltransferase: “Crystal structure of human T-protein of glycine cleavage system”. X-ray diffraction, 2 ligands (THH, SO4), 6 pockets (best druggability 0.80). MolNFT v1 #26556 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1WSV
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminomethyltransferase
- EC
- 2.1.2.10
- UniProt
- P48728
- Ligands
- THH, SO4
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminomethyltransferase (EC 2.1.2.10) | protein | 371 | 25% helix, 33% strand | P48728 |
Ligands and binding sites
- THH · N-[4-({[(6S)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.80 | 0.95 | 38 | empty |
| 2 | 443 | 0.72 | 0.82 | 60 | THH |
| 3 | 469 | 0.72 | 0.81 | 60 | THH |
| 4 | 265 | 0.51 | 0.75 | 35 | empty |
| 5 | 200 | 0.45 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 983 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1WSV · Crystal Structure of Human T-protein of Glycine Cleavage System · the same entry in another collection · chain A against A, TM-score 1.00
- P48728 · AlphaFold monomer V2.0 prediction for aminomethyltransferase, mitochondrial (P48728) · a predicted model of the same protein · chain B 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 P48728
- Elsewhere: RCSB PDB 1WSV · PDBe 1WSV · UniProt P48728
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