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3c5v

PP2A-specific methylesterase apo form (PME)

Method: X-RAY DIFFRACTION Dmax: 59.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein phosphatase methylesterase 1

Homo sapiens

UniProt Q9Y570

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 39–248 Chain A； UniProt 281–386 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；26% v/v Jeffamine-2001, 200mM sodium chloride, 5mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.00 Å R-free 0.220

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3C5V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3C5W Complex between PP2A-specific methylesterase PME-1 and PP2A core enzyme Deposited 2008-02-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 39–238（200 aa）
Chain P 284–386（103 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；290 K；25% w/v PEG3350, 100 mM ammonium citrate, and 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.80 Å R-free 0.263
7SOY The structure of the PP2A-B56gamma1 holoenzyme-PME-1 complex Deposited 2021-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain P 1–386（386 aa）
Mutation：S156A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPME1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–210； UniProt 39–248 Author chain A； PDBConstruct 211–316； UniProt 281–386

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3c5v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3c5v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3c5v
Deposition date deposition_date2008-02-01
Structure title titlePP2A-specific methylesterase apo form (PME)
Keywords keywordsdemethylase, PP2A, Alternative splicing, Hydrolase, Phosphoprotein, Serine esterase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier19.27 Å
Radius of gyration Rg (electron density) rg_electron18.00 Å
Forward intensity I(0) i018214700.00
Molecular weight molecular_weight32447.0 kDa
Excluded volume excluded_volume40682 ų
Envelope volume envelope_volume45903 ų
Hydration-shell volume shell_volume20682 ų
Envelope diameter envelope_diameter61.6 Å
Shell Rg shell_rg25.00 Å
Envelope Rg envelope_rg18.32 Å
Shape Rg shape_rg17.99 Å
Total Rg total_rg19.03 Å
Total atoms total_atoms2278
Residues n_residues294
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.8 Å
Rg (real space) rg_real19.11 Å
Rg uncertainty (real space) rg_real_error0.25 Å
I(0) (real space) i0_real1.8210e+07
I(0) uncertainty (real space) i0_real_error1.9890e+05
Rg (reciprocal space) rg_reciprocal19.13 Å
I(0) (reciprocal space) i0_reciprocal18210000.0000
Solution quality estimate total_estimate0.8950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.465
Angular range angular_range— – 0.4150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5763000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.989
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3c5vA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
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8. Citations (1)

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9. Files and Curves (10)