9r8q

Structure of thrombin bound to BAY 3389934

Method: X-RAY DIFFRACTION

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

Prothrombin

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-2 × 1 （P28504） ;2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GLYCEROL × 3 DIMETHYL SULFOXIDE × 4 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, 2
Chains and sequence ranges	Author chain L； PDBConstruct 1–29； UniProt 333–361 Author chain H； PDBConstruct 1–259； UniProt 364–622

Hirudin-2

Hirudo medicinalis

UniProt P28504

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Prothrombin × 1 （P00734） Prothrombin × 1 （P00734） ;2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GLYCEROL × 3 DIMETHYL SULFOXIDE × 4 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIR2_HIRME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–11； UniProt 54–64

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	9r8q
Deposition date deposition_date	2025-05-16
Structure title title	Structure of thrombin bound to BAY 3389934
Keywords keywords	Blood coagulation, Protease, HYDROLASE; HYDROLASE
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.

9r8q__assembly_1__model_1

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

Download this curve (.dat)

9r8q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r8q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.25 Å
Rg (electron density)	18.07 Å
Total Rg	19.10 Å
Atom count	2435
Residues	287
Excluded volume	43311 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r8q__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 (8)

Entity 1 Entity 1 polymer

Description description	Prothrombin
Molecular weight formula_weight	3432.8 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
Atom count atom_count	2666

EADCGLRPLFEKKSLEDKTERELLESYID

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Bos taurus

Entity 2 Entity 2 polymer

Description description	Prothrombin
Molecular weight formula_weight	29780.2 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

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Bos taurus

Entity 3 Entity 3 polymer

Description description	Hirudin-2
Molecular weight formula_weight	1420.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GDFEEIPEEYL

Source Source

Source organism organism	Hirudo medicinalis
Common name common_name	medicinal leech
NCBI taxonomy ID ncbi_taxonomy_id	6421
Host organism host_organism	synthetic construct

Entity 4 Entity 4 non-polymer

Description description	;2-(1-methylimidazol-2-yl)ethyl (2~{S})-3-[(5-chloranylthiophen-2-yl)carbonylamino]-2-[[2-ethyl-3-[(3~{S})-3-oxidanyl-2-oxidanylidene-pyrrolidin-1-yl]phenyl]sulfonylamino]propanoate ;
Molecular weight formula_weight	624.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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Unit-cell length a length_a	69.766 Å
Unit-cell length b length_b	71.817 Å
Unit-cell length c length_c	72.026 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.97 °
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	monoclinic

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	23.650 Å
R factor r_factor	0.1772
R_work r_work	0.1759
R_free r_free	0.2003

Structure of thrombin bound to BAY 3389934

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

Prothrombin

State in the Current Structure

Other States of the Same Protein in the Database

Hirudin-2

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

9r8q__assembly_1__model_1

9r8q__assembly_1__model_1 | I(q)

9r8q__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Structure of thrombin bound to BAY 3389934

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

Prothrombin

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-2

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

9r8q__assembly_1__model_1

9r8q__assembly_1__model_1 | I(q)

9r8q__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 water

7. Citations (1)