SAXSdb — 2v3h

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

THROMBIN HEAVY CHAIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HIRUDIN IIA × 1 （P28503） (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID × 1 SODIUM ION × 1 CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THRB_HUMAN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain H； PDBConstruct 1–257； UniProt 364–620 Author chain L； PDBConstruct 1–28； UniProt 334–361

HIRUDIN IIA

OrganismNot specified

UniProt P28503

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	THROMBIN HEAVY CHAIN × 1 （P00734） THROMBIN LIGHT CHAIN × 1 （P00734） (2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID × 1 SODIUM ION × 1 CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITHC_HIRME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 2–11； UniProt 56–65

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2v3h
Deposition date deposition_date	2007-06-18
Structure title title	Thrombin with 3-cycle no F
Keywords keywords	;SERINE PROTEASE INHIBITOR COMPLEX, BLOOD CLOTTING, GAMMA-CARBOXYGLUTAMIC ACID, SERINE PROTEASE, CALCIUM-BINDING, DISEASE MUTATION, BLOOD COAGULATION, SULFATION, ACUTE PHASE, GLYCOPROTEIN, PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2v3h__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2v3h__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v3h__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.04 Å
Rg (electron density)	17.84 Å
Total Rg	18.89 Å
Atom count	2340
Residues	283
Excluded volume	41808 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v3h__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	THROMBIN HEAVY CHAIN
Molecular weight formula_weight	29594.1 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	2754

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	CRICETULUS GRISEUS

Entity 2 Entity 2 polymer

Description description	HIRUDIN IIA
Molecular weight formula_weight	1396.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

XFEEIPEEYLQ

Entity 3 Entity 3 polymer

Description description	THROMBIN LIGHT CHAIN
Molecular weight formula_weight	3303.7 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ADCGLRPLFEKKSLEDKTERELLESYID

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	CRICETULUS GRISEUS

Entity 4 Entity 4 non-polymer

Description description	(2R)-({4-[AMINO(IMINO)METHYL]PHENYL}AMINO){3-[3-(DIMETHYLAMINO)-2,2-DIMETHYLPROPOXY]-5-ETHYLPHENYL}ACETIC ACID
Molecular weight formula_weight	426.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	392

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2v3hH01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2v3hH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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Unit-cell length a length_a	70.440 Å
Unit-cell length b length_b	71.780 Å
Unit-cell length c length_c	72.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.790 Å
Low-resolution limit resolution_low	71.250 Å
R factor r_factor	0.1750
R_work r_work	0.1730
R_free r_free	0.2070

Thrombin with 3-cycle no F

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

THROMBIN HEAVY CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

HIRUDIN IIA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2v3h__assembly_1__model_1

2v3h__assembly_1__model_1 | I(q)

2v3h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Thrombin with 3-cycle no F

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

THROMBIN HEAVY CHAIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIRUDIN IIA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2v3h__assembly_1__model_1

2v3h__assembly_1__model_1 | I(q)

2v3h__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)