5bzz

Crystal structure of human phosphatase PTEN in its reduced state

Method: X-RAY DIFFRACTION Dmax: 141.8 Å Quality: GOOD

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

Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN

Homo sapiens

UniProt P60484

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 14–351 Fragment:PTEN wt 7-353 delta 286-309 Mutation:Deletion 286-309 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol Resolution 2.20 Å R-free 0.221
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 14–351 Fragment:PTEN wt 7-353 delta 286-309 Mutation:Deletion 286-309 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol Resolution 2.20 Å R-free 0.221
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 14–351 Fragment:PTEN wt 7-353 delta 286-309 Mutation:Deletion 286-309 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol Resolution 2.20 Å R-free 0.221
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 14–351 Fragment:PTEN wt 7-353 delta 286-309 Mutation:Deletion 286-309 TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.1 M MES pH 6.5, 1.25 M L-tartrate, 7.5% glycerol Resolution 2.20 Å R-free 0.221

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.

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTEN_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–314; UniProt 14–351 Author chain B; PDBConstruct 1–314; UniProt 14–351 Author chain C; PDBConstruct 1–314; UniProt 14–351 Author chain D; PDBConstruct 1–314; UniProt 14–351

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 5bzz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5bzz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5bzz
Deposition date deposition_date2015-06-11
Structure title titleCrystal structure of human phosphatase PTEN in its reduced state
Keywords keywordsphosphatase, C2 domain, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.95
Radius of gyration Rg (electron density) rg_electron43.58
Forward intensity I(0) i0306639000.00
Molecular weight molecular_weight146980.0 kDa
Excluded volume excluded_volume185050 ų
Envelope volume envelope_volume256350 ų
Hydration-shell volume shell_volume51610 ų
Envelope diameter envelope_diameter151.2
Shell Rg shell_rg45.45
Envelope Rg envelope_rg43.08
Shape Rg shape_rg43.58
Total Rg total_rg43.68
Total atoms total_atoms10378
Residues n_residues1256
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 dmax141.8
Rg (real space) rg_real44.01
Rg uncertainty (real space) rg_real_error1.46
I(0) (real space) i0_real3.0660e+08
I(0) uncertainty (real space) i0_real_error5.4280e+06
Rg (reciprocal space) rg_reciprocal43.95
I(0) (reciprocal space) i0_reciprocal306600000.0000
Solution quality estimate total_estimate0.8741
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.0
Skewness Skewness skewness0.247
Kurtosis Kurtosis kurtosis-0.554
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30040000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.653

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5bzza1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamilyc.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family familyc.45.1.1 — Dual specificity phosphatase-like
Domain ID domain_idd5bzza2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.1 — PLC-like (P variant)
Domain ID domain_idd5bzzb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamilyc.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family familyc.45.1.1 — Dual specificity phosphatase-like
Domain ID domain_idd5bzzb2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.1 — PLC-like (P variant)
Domain ID domain_idd5bzzc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamilyc.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family familyc.45.1.1 — Dual specificity phosphatase-like
Domain ID domain_idd5bzzc2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.1 — PLC-like (P variant)
Domain ID domain_idd5bzzd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamilyc.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family familyc.45.1.1 — Dual specificity phosphatase-like
Domain ID domain_idd5bzzd2
Class classb — All beta proteins
Fold Fold foldb.7 — C2 domain-like
Superfamily Superfamily superfamilyb.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family familyb.7.1.1 — PLC-like (P variant)

CATH v4.4 (8 domains)

Domain ID domain_id5bzzA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily
Domain ID domain_id5bzzA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1110
Domain ID domain_id5bzzB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily
Domain ID domain_id5bzzB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1110
Domain ID domain_id5bzzC01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily
Domain ID domain_id5bzzC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1110
Domain ID domain_id5bzzD01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily
Domain ID domain_id5bzzD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1110

8. Citations (1)

9. Files and Curves (10)