Research workbench
Plasmodium vivax shmt bound with plp-glycine and GS625
Analyse Plasmodium vivax shmt bound with plp-glycine and GS625 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFY
- 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, 8UL, CL
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Serine hydroxymethyltransferase (EC 2.1.2.1) | protein | 442 | 49% 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
- 8UL · 1-[3-[(4~{S})-6-azanyl-5-cyano-3-methyl-4-propan-2-yl-2~{H}-pyrano[2,3-c]pyrazol-4-yl]-5-fluoranyl-phenyl]piperidine-4-carboxylic acid · 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.77 | 0.87 | 54 | PLG, 8UL |
| 2 | 415 | 0.76 | 0.85 | 55 | PLG, 8UL |
| 3 | 72 | 0.74 | 0.98 | 20 | empty |
| 4 | 877 | 0.73 | 0.77 | 66 | empty |
| 5 | 168 | 0.48 | 0.77 | 30 | PLG, 8UL |
Interfaces
2 interfaces between chains.
- A–B · 4711 Ų buried · 68 hydrogen bonds · protein-protein
- B–C · 362 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5YFY · Plasmodium vivax SHMT bound with PLP-glycine and GS625 · 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 5YFY · PDBe 5YFY · UniProt A0A1G4H5I1
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