MolNFT v1 · #64456 · protein
Crystal structure of a eukaryotic polyphosphate polymerase in complex with appnhp-MN2+
3G3R · Vacuolar transporter chaperone 4: “Crystal structure of a eukaryotic polyphosphate polymerase in complex with appnhp-MN2+”. X-ray diffraction, 4 ligands (ANP, MN, NA), 9 pockets (best druggability 0.72). MolNFT v1 #64456 on…
- PDB
- 3G3R
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar transporter chaperone 4
- UniProt
- P47075
- Ligands
- ANP, MN, NA, SO4
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar transporter chaperone 4 | protein | 286 | 28% helix, 33% strand | P47075 |
| B | Vacuolar transporter chaperone 4 | protein | 285 | 28% helix, 32% strand | P47075 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.72 | 0.80 | 58 | ANP, MN |
| 2 | 357 | 0.70 | 0.83 | 44 | ANP, MN, SO4 |
| 3 | 112 | 0.41 | 0.76 | 16 | empty |
| 4 | 102 | 0.40 | 0.76 | 16 | empty |
| 5 | 122 | 0.39 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3G3R · Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- P47075 · AlphaFold monomer V2.0 prediction for vacuolar transporter chaperone 4 (P47075) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P47075
- Elsewhere: RCSB PDB 3G3R · PDBe 3G3R · UniProt P47075
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