MolNFT v1 · #140602 · protein
Plasmodium vivax shmt bound with plp-glycine and S-GS834
5YG3 · Serine hydroxymethyltransferase: “Plasmodium vivax shmt bound with plp-glycine and S-GS834”. X-ray diffraction, 3 ligands (PLG, 8UC, CL), 13 pockets (best druggability 0.78). MolNFT v1 #140602 on GenesisL1: 3D structure, binding…
- PDB
- 5YG3
- Type
- protein
- Length
- 1,326 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase
- EC
- 2.1.2.1
- UniProt
- A0A1G4H5I1
- Ligands
- PLG, 8UC, CL
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 442 | 48% helix, 13% strand | A0A1G4H5I1 |
Ligands and binding sites
- PLG · N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane] · ligand · 3 copies · chains A, B, C
- 8UC · (3~{S})-6'-azanyl-7-fluoranyl-2,2,3'-trimethyl-5-pyridin-4-yl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5'-carbonitrile · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.78 | 0.88 | 52 | PLG, 8UC |
| 2 | 503 | 0.76 | 0.84 | 65 | PLG, 8UC |
| 3 | 78 | 0.75 | 0.98 | 22 | empty |
| 4 | 829 | 0.72 | 0.77 | 61 | empty |
| 5 | 182 | 0.51 | 0.78 | 35 | PLG, 8UC |
Interfaces
2 interfaces between chains.
- A–B · 4723 Ų buried · 59 hydrogen bonds · protein-protein
- B–C · 387 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YG3 · Plasmodium vivax SHMT bound with PLP-glycine and S-GS834 · 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 A0A1G4H5I1
- Elsewhere: RCSB PDB 5YG3 · PDBe 5YG3 · UniProt A0A1G4H5I1
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