MolNFT v1 · #123468 · protein
Crystal structure of plasmodium falciparum PF3D7_0606800 (PFVFT1)
5JKQ: “Crystal structure of plasmodium falciparum PF3D7_0606800 (PFVFT1)”. X-ray diffraction, 1 ligand (SO4), 16 pockets (best druggability 0.83). MolNFT v1 #123468 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JKQ
- Type
- protein
- Length
- 1,099 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PFVFT1
- UniProt
- C6KSR6
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PFVFT1 | protein | 281 | 33% helix, 22% strand | C6KSR6 |
| B | PFVFT1 | protein | 282 | 38% helix, 20% strand | C6KSR6 |
| D | PFVFT1 | protein | 263 | 38% helix, 22% strand | C6KSR6 |
| C | PFVFT1 | protein | 273 | 36% helix, 22% strand | C6KSR6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.83 | 0.95 | 32 | empty |
| 2 | 700 | 0.71 | 0.78 | 62 | empty |
| 3 | 498 | 0.64 | 0.77 | 71 | empty |
| 4 | 253 | 0.61 | 0.81 | 31 | empty |
| 5 | 200 | 0.56 | 0.79 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1612 Ų buried · 14 hydrogen bonds · protein-protein
- D–C · 1161 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 409 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 349 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 5JKQ · Crystal structure of Plasmodium falciparum Pf3D7_0606800 (PfVFT1) · 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 C6KSR6
- Elsewhere: RCSB PDB 5JKQ · PDBe 5JKQ · UniProt C6KSR6
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