1q6s

THE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH COMPOUND 9

Method: X-RAY DIFFRACTION Dmax: 97.5 Å Quality: GOOD

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

Protein-tyrosine phosphatase, non-receptor type 1

Homo sapiens

UniProt P18031

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 1–298 Fragment:CATALYTIC DOMAIN CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 214 6-[4-((2R)-2-(1H-1,2,3-BENZOTRIAZOL-1-YL)-3-{4-[DIFLUORO(PHOSPHONO)METHYL]PHENYL}-2-PHENYLPROPYL)PHENYL]-2-METHYLQUINOLIN-8-YLPHOSPHONIC ACID × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;PEG 3350, MGCL2, HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.233
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–298 Fragment:CATALYTIC DOMAIN CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 214 6-[4-((2R)-2-(1H-1,2,3-BENZOTRIAZOL-1-YL)-3-{4-[DIFLUORO(PHOSPHONO)METHYL]PHENYL}-2-PHENYLPROPYL)PHENYL]-2-METHYLQUINOLIN-8-YLPHOSPHONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;277 K;PEG 3350, MGCL2, HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.20 Å R-free 0.233

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.

440 other PDB entries and 468 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 13–310; UniProt 1–298 Author chain B; PDBConstruct 13–310; UniProt 1–298

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 1q6s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1q6s
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1q6s
Deposition date deposition_date2003-08-13
Structure title titleTHE STRUCTURE OF PHOSPHOTYROSINE PHOSPHATASE 1B IN COMPLEX WITH COMPOUND 9
Keywords keywordsPHOSPHATASE, SECONDARY BINDING SITE, SELECTIVITY, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.06
Radius of gyration Rg (electron density) rg_electron27.33
Forward intensity I(0) i076900600.00
Molecular weight molecular_weight68603.0 kDa
Excluded volume excluded_volume85619 ų
Envelope volume envelope_volume101380 ų
Hydration-shell volume shell_volume31003 ų
Envelope diameter envelope_diameter103.3
Shell Rg shell_rg34.34
Envelope Rg envelope_rg27.71
Shape Rg shape_rg27.33
Total Rg total_rg28.00
Total atoms total_atoms4815
Residues n_residues578
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 dmax97.5
Rg (real space) rg_real28.15
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real7.6900e+07
I(0) uncertainty (real space) i0_real_error1.2710e+06
Rg (reciprocal space) rg_reciprocal28.13
I(0) (reciprocal space) i0_reciprocal76900000.0000
Solution quality estimate total_estimate0.8629
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.423
Kurtosis Kurtosis kurtosis-0.321
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha25620000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.775; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.911; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1q6sa1
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.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases
Domain ID domain_idd1q6sa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd1q6sb1
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.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases
Domain ID domain_idd1q6sb2
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_id1q6sA00
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_id1q6sB00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily10 — Protein tyrosine phosphatase superfamily

8. Citations (1)

9. Files and Curves (10)