Research workbench
Crystal structure of an rb C-terminal peptide bound to the catalytic subunit of PP1
Analyse Crystal structure of an rb C-terminal peptide bound to the catalytic subunit of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3N5U
- Type
- protein
- Length
- 595 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit…
- EC
- 3.1.3.16
- UniProt
- P62136, P06400
- Ligands
- MN, CL
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) | protein | 294 | 33% helix, 18% strand | P62136 |
| C | Retinoblastoma-associated protein | protein | 7 | 0% helix, 29% strand | P06400 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 504 | 0.73 | 0.82 | 60 | empty |
| 2 | 118 | 0.41 | 0.76 | 24 | MN, CL |
| 3 | 115 | 0.40 | 0.76 | 24 | CL |
| 4 | 83 | 0.33 | 0.75 | 20 | empty |
| 5 | 67 | 0.29 | 0.74 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–B · 753 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 519 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3N5U · Crystal structure of an Rb C-terminal peptide bound to the catalytic subunit of PP1 · the same entry in another collection · chain A against A, TM-score 1.00
- P62136 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PP1-alpha… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P06400 · AlphaFold monomer V2.0 prediction for retinoblastoma-associated protein (P06400) · a predicted model of the same protein · chain C against A, TM-score 0.47
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 P62136
- Every structure of UniProt P06400
- Elsewhere: RCSB PDB 3N5U · PDBe 3N5U · UniProt P62136 · UniProt P06400
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