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2ocv

Structural basis of Na+ activation mimicry in murine thrombin

Method: X-RAY DIFFRACTION Dmax: 64.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thrombin

Mus musculus

UniProt P19221

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 1 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 319–360 Chain B； UniProt 361–618 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；295 K；25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50 Resolution 2.20 Å R-free 0.246
2 Other combination Homooligomer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 319–360 Chain B； UniProt 361–618 Not recorded 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；295 K；25% PEG 2000 MME, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50 Resolution 2.20 Å R-free 0.246

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 2OCV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2PUX Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR3 Deposited 2007-05-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 317–360（44 aa）
Chain B 361–618（258 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；20% PEG 10000, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.00 Å R-free 0.225
2PV9 Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4 Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 317–360（44 aa）
Chain B 361–618（258 aa）
Mutation：S195A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；20% PEG 3350, 200 mM MgSO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.50 Å R-free 0.319
2PV9 Crystal structure of murine thrombin in complex with the extracellular fragment of murine PAR4 Deposited 2007-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 317–360（44 aa）
Chain B 361–618（258 aa）
Mutation：S195A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295 K；20% PEG 3350, 200 mM MgSO4, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.50 Å R-free 0.319
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 317–360（44 aa）
Chain B 361–618（258 aa）
Mutation：W215A, E217A SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.40 Å R-free 0.243
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 317–360（44 aa）
Chain D 361–618（258 aa）
Mutation：W215A, E217A SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.40 Å R-free 0.243
3EDX Crystal structure of the W215A/E217A mutant of murine thrombin Deposited 2008-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 317–360（44 aa）
Chain F 361–618（258 aa）
Mutation：W215A, E217A SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；0.2M NA2SO4, 20 % PEG 3350, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.40 Å R-free 0.243
3HK3 Crystal structure of murine thrombin mutant W215A/E217A (one molecule in the asymmetric unit) Deposited 2009-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 317–360（44 aa） Fragment：Light chain: UNP residues 317-360
Chain B 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618
Mutation：W215A, E217A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；295 K；200mM Ammonium chloride, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.94 Å R-free 0.235
3HK6 Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit) Deposited 2009-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 317–360（44 aa） Fragment：Light chain: UNP residues 317-360
Chain B 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618
Mutation：W215A, E217A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；200mM Ammonium dihydrogen phosphate, 14% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.20 Å R-free 0.314
3HK6 Crystal structure of murine thrombin mutant W215A/E217A (two molecules in the asymmetric unit) Deposited 2009-05-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 317–360（44 aa） Fragment：Light chain: UNP residues 317-360
Chain D 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618
Mutation：W215A, E217A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；200mM Ammonium dihydrogen phosphate, 14% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.20 Å R-free 0.314
3HKI Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 317–360（44 aa） Fragment：Light chain: UNP residues 317-360
Chain B 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618
Mutation：W215A, E217A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM Tris-HCl pH 8.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.20 Å R-free 0.261
3HKI Crystal structure of murine thrombin mutant W215A/E217A in complex with the extracellular fragment of human PAR1 Deposited 2009-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 317–360（44 aa） Fragment：Light chain: UNP residues 317-360
Chain E 361–618（258 aa） Fragment：Heavy chain: UNP residues 361-618
Mutation：W215A, E217A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；100mM Tris-HCl pH 8.5, 20% PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.20 Å R-free 0.261

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THRB_MOUSE
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 15–28； UniProt 319–360 Author chain B； PDBConstruct 1–258； UniProt 361–618

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 2ocv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ocv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ocv
Deposition date deposition_date2006-12-21
Structure title titleStructural basis of Na+ activation mimicry in murine thrombin
Keywords keywordsSERINE PROTEASE, HYDROLASE; 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_guinier19.33 Å
Radius of gyration Rg (electron density) rg_electron18.20 Å
Forward intensity I(0) i018650700.00
Molecular weight molecular_weight33643.0 kDa
Excluded volume excluded_volume42502 ų
Envelope volume envelope_volume48215 ų
Hydration-shell volume shell_volume21366 ų
Envelope diameter envelope_diameter68.8 Å
Shell Rg shell_rg25.36 Å
Envelope Rg envelope_rg18.65 Å
Shape Rg shape_rg18.16 Å
Total Rg total_rg19.32 Å
Total atoms total_atoms2369
Residues n_residues237
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 dmax64.7 Å
Rg (real space) rg_real19.19 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real1.8650e+07
I(0) uncertainty (real space) i0_real_error2.6050e+05
Rg (reciprocal space) rg_reciprocal19.21 Å
I(0) (reciprocal space) i0_reciprocal18650000.0000
Solution quality estimate total_estimate0.6291
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary25.5 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.222
Angular range angular_range— – 0.4100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7689000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.710; Stabil: 0.992; Sysdev: 0.356; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2ocvB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id2ocvB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
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8. Citations (2)

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9. Files and Curves (10)