Research workbench
Crystal structure of the leucine zipper of human PRKCBP1
Analyse Crystal structure of the leucine zipper of human PRKCBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MQ4
- Type
- protein
- Length
- 674 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase C-binding protein 1
- UniProt
- Q9ULU4
- Ligands
- ZN, SO4
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase C-binding protein 1 | protein | 113 | 73% helix, 9% strand | Q9ULU4 |
| B, D, E, F | Protein kinase C-binding protein 1 | protein | 111 | 75% helix, 9% strand | Q9ULU4 |
| C | Protein kinase C-binding protein 1 | protein | 117 | 70% helix, 9% strand | Q9ULU4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, E, F, B, D, C
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 | 408 | 0.64 | 0.78 | 37 | empty |
| 2 | 333 | 0.59 | 0.77 | 48 | empty |
| 3 | 74 | 0.47 | 0.83 | 16 | empty |
| 4 | 152 | 0.46 | 0.76 | 22 | empty |
| 5 | 57 | 0.44 | 0.83 | 12 | empty |
Interfaces
10 interfaces between chains.
- A–D · 2150 Ų buried · 13 hydrogen bonds · protein-protein
- B–F · 2010 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1920 Ų buried · 11 hydrogen bonds · protein-protein
- D–F · 1223 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 1052 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MQ4 · Crystal Structure of the leucine zipper of human PRKCBP1 · the same entry in another collection · chain F against F, TM-score 1.00
- Q9ULU4 · AlphaFold monomer V2.0 prediction for protein kinase C-binding protein 1 (Q9ULU4) · a predicted model of the same protein · chain B against A, TM-score 0.80
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 Q9ULU4
- Elsewhere: RCSB PDB 5MQ4 · PDBe 5MQ4 · UniProt Q9ULU4
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