MolNFT v1 · #104929 · protein
2.7 ångström structure of a phosphotransferase in complex with a receiver domain
4QPJ: “2.7 ångström structure of a phosphotransferase in complex with a receiver domain”. X-ray diffraction, 4 ligands (CA, NA, MG), 4 pockets (best druggability 0.83). MolNFT v1 #104929 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QPJ
- Type
- protein
- Length
- 658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotransferase; Cell cycle response regulator ctra
- UniProt
- Q2YQA5, Q2YQA4
- Ligands
- CA, NA, MG, CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotransferase | protein | 208 | 51% helix, 18% strand | Q2YQA5 |
| B | Phosphotransferase | protein | 209 | 50% helix, 18% strand | Q2YQA5 |
| C | Cell cycle response regulator ctra | protein | 120 | 45% helix, 20% strand | Q2YQA4 |
| D | Cell cycle response regulator ctra | protein | 121 | 38% helix, 21% strand | Q2YQA4 |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A
- MG · Magnesium ion · metal · chains D
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.83 | 0.84 | 98 | GOL, CL |
| 2 | 1136 | 0.82 | 0.83 | 111 | GOL, NA |
| 3 | 131 | 0.44 | 0.77 | 22 | empty |
| 4 | 53 | 0.33 | 0.78 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1546 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 995 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 903 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 274 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4QPJ · 2.7 Angstrom Structure of a Phosphotransferase in Complex with a Receiver Domain · the same entry in another collection · chain D against D, TM-score 1.00
- Q2YQA5 · AlphaFold monomer V2.0 prediction for protein phosphotransferase chpt (Q2YQA5) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q2YQA4 · AlphaFold monomer V2.0 prediction for cell cycle response regulator ctra (Q2YQA4) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q2YQA5
- Every structure of UniProt Q2YQA4
- Elsewhere: RCSB PDB 4QPJ · PDBe 4QPJ · UniProt Q2YQA5 · UniProt Q2YQA4
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