Research workbench
Crystal structure of the complex of lcmt-1 and PP2A
Analyse Crystal structure of the complex of lcmt-1 and PP2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P71
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine carboxyl methyltransferase 1; SERINE/THREONINE-protein phosphatase 2A catalytic…
- EC
- 2.1.1.-, 3.1.3.16
- UniProt
- Q9UIC8, P67775
- Ligands
- AN6, MN
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) | protein | 315 | 49% helix, 15% strand | Q9UIC8 |
| C | SERINE/THREONINE-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) | protein | 303 | 34% helix, 17% strand | P67775 |
Ligands and binding sites
- AN6 · 5'-{[(3S)-3-amino-3-carboxypropyl](ethyl)amino}-5'-deoxyadenosine · ligand · chains T, C
- MN · Manganese (II) ion · metal · 2 copies · chains C, T
- PEG · Di(hydroxyethyl)ether · additive · chains T
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.79 | 0.95 | 32 | AN6 |
| 2 | 313 | 0.67 | 0.82 | 34 | empty |
| 3 | 154 | 0.61 | 0.84 | 33 | empty |
| 4 | 95 | 0.39 | 0.76 | 15 | empty |
| 5 | 70 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- T–C · 1564 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3P71 · Crystal structure of the complex of LCMT-1 and PP2A · the same entry in another collection · chain T against T, TM-score 1.00
- Q9UIC8 · AlphaFold monomer V2.0 prediction for leucine carboxyl methyltransferase 1 (Q9UIC8) · a predicted model of the same protein · chain T against A, TM-score 1.00
- P67775 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase 2A catalytic… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9UIC8
- Every structure of UniProt P67775
- Elsewhere: RCSB PDB 3P71 · PDBe 3P71 · UniProt Q9UIC8 · UniProt P67775
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