6alz

Crystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin

Method: X-RAY DIFFRACTION Dmax: 87.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Homo sapiens

UniProt P62136

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 7–300 Fragment:residues 7-300 MN MANGANESE (II) ION × 2 BKM (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid × 1 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0 Resolution 2.21 Å R-free 0.216
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 7–300 Fragment:residues 7-300 MN MANGANESE (II) ION × 2 BKM (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0 Resolution 2.21 Å R-free 0.216
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 7–300 Chain B; UniProt 7–300 Fragment:residues 7-300 MN MANGANESE (II) ION × 4 BKM (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid × 2 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0 Resolution 2.21 Å R-free 0.216

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.

45 other PDB entries and 86 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–299; UniProt 7–300 Author chain B; PDBConstruct 6–299; UniProt 7–300

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 6alz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6alz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6alz
Deposition date deposition_date2017-08-08
Structure title titleCrystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin
Keywords keywordsInhibitor, complex, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.46
Radius of gyration Rg (electron density) rg_electron26.75
Forward intensity I(0) i072997800.00
Molecular weight molecular_weight68007.0 kDa
Excluded volume excluded_volume85400 ų
Envelope volume envelope_volume98698 ų
Hydration-shell volume shell_volume30961 ų
Envelope diameter envelope_diameter92.1
Shell Rg shell_rg33.91
Envelope Rg envelope_rg26.75
Shape Rg shape_rg26.73
Total Rg total_rg27.54
Total atoms total_atoms4764
Residues n_residues587
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax87.5
Rg (real space) rg_real27.49
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real7.3000e+07
I(0) uncertainty (real space) i0_real_error1.1230e+06
Rg (reciprocal space) rg_reciprocal27.49
I(0) (reciprocal space) i0_reciprocal73000000.0000
Solution quality estimate total_estimate0.8964
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary86.0
Skewness Skewness skewness0.348
Kurtosis Kurtosis kurtosis-0.534
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29640000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd6alza_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd6alzb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd6alzb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id6alzA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id6alzB00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases

8. Citations (1)

9. Files and Curves (10)