MolNFT v1 · #103399 · protein
Crystal structure of plasmodium vivax shmt with L-serine schiff base
4PFN · Serine hydroxymethyltransferase, putative: “Crystal structure of plasmodium vivax shmt with L-serine schiff base”. X-ray diffraction, 3 ligands (PLP, SER, CL), 13 pockets (best druggability 0.76). MolNFT v1 #103399 on GenesisL1: 3D…
- PDB
- 4PFN
- Type
- protein
- Length
- 1,326 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine hydroxymethyltransferase, putative
- UniProt
- A5K8L9
- Ligands
- PLP, SER, CL
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Serine hydroxymethyltransferase, putative | protein | 442 | 49% helix, 13% strand | A5K8L9 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 3 copies · chains A, B, C
- SER · Serine · 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 | 422 | 0.76 | 0.85 | 68 | PLP, SER |
| 2 | 358 | 0.75 | 0.86 | 55 | PLP, SER |
| 3 | 72 | 0.75 | 0.99 | 23 | empty |
| 4 | 342 | 0.66 | 0.81 | 34 | empty |
| 5 | 525 | 0.65 | 0.76 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–B · 4620 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 432 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4PFN · Crystal structure of Plasmodium vivax SHMT with L-serine Schiff base · 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 A5K8L9
- Elsewhere: RCSB PDB 4PFN · PDBe 4PFN · UniProt A5K8L9
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