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Human PP2CALPHA (PPM1A) complexed with cyclic peptide C(MPSIPYVA)

Analyse Human PP2CALPHA (PPM1A) complexed with cyclic peptide C(MPSIPYVA) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6B67
Type: protein
Length: 906 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein phosphatase 1A; Cyclic peptide C(MPSIPYVA)
EC: 3.1.3.16
UniProt: P35813
Ligands: 48V, CA
Pockets: 11 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Protein phosphatase 1A (EC 3.1.3.16)	protein	296	30% helix, 33% strand	P35813
D, E, F	Cyclic peptide C(MPSIPYVA)	protein	6	0% helix, 0% strand	—

Ligands and binding sites

48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 3 copies · chains A, D, B, E, C, F
CA · Calcium ion · metal · 10 copies · chains A, D, B, E, C, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1065	0.83	0.84	75	empty
2	740	0.68	0.76	71	empty
3	117	0.54	0.82	15	empty
4	62	0.47	0.84	14	empty
5	108	0.47	0.80	24	CA

Interfaces

5 interfaces between chains.

B–C · 849 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 583 Å² buried · 15 hydrogen bonds · protein-protein
B–E · 516 Å² buried · 13 hydrogen bonds · protein-protein
A–D · 490 Å² buried · 11 hydrogen bonds · protein-protein
C–F · 410 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 covalent, 6 modified (covalent ligand, phosphorylation).

Compared structures

6B67 · Human PP2Calpha (PPM1A) complexed with cyclic peptide c(MpSIpYVA) · the same entry in another collection · chain C against C, TM-score 1.00
P35813 · AlphaFold monomer V2.0 prediction for protein phosphatase 1A (P35813) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P35813
Elsewhere: RCSB PDB 6B67 · PDBe 6B67 · UniProt P35813

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