5ahg

Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine

Method: X-RAY DIFFRACTION

▼

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

THROMBIN HEAVY CHAIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HIRUDIN VARIANT-2 × 1 （P28511） SODIUM ION × 2 DIMETHYL SULFOXIDE × 2 PHOSPHATE ION × 1 GLYCEROL × 1 ((4-Chlorophenyl)sulfamoyl))dimethylamine × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 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 1–258； UniProt 364–621 Author chain L； PDBConstruct 1–29； UniProt 333–361

HIRUDIN VARIANT-2

OrganismNot specified

UniProt P28511

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） SODIUM ION × 2 DIMETHYL SULFOXIDE × 2 PHOSPHATE ION × 1 GLYCEROL × 1 ((4-Chlorophenyl)sulfamoyl))dimethylamine × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIR3C_HIRME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–12； UniProt 54–65

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ahg
Deposition date deposition_date	2015-02-06
Structure title title	Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine
Keywords keywords	;HYDROLASE, HYDROLASE INHIBITOR COMPLEX, SERINE PROTEASE, BLOOD COAGULATION, BLOOD CLOTTING, CONVERTION OF FIBRINOGEN TO FIBRIN, BLOOD CLOTTING INHIBITOR, THROMBIN INHIBITOR, FRAGMENT, GLYCOSYLATION, BLOOD ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5ahg__assembly_1__model_1

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

Download this curve (.dat)

5ahg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ahg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.01 Å
Rg (electron density)	17.83 Å
Total Rg	18.82 Å
Atom count	4472
Residues	289
Excluded volume	42088 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ahg__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	THROMBIN HEAVY CHAIN
Molecular weight formula_weight	29651.1 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	4949

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFG

Entity 2 Entity 2 polymer

Description description	HIRUDIN VARIANT-2
Molecular weight formula_weight	1548.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

GDFEEIPEEYLQ

Entity 3 Entity 3 polymer

Description description	THROMBIN LIGHT CHAIN
Molecular weight formula_weight	3432.8 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

EADCGLRPLFEKKSLEDKTERELLESYID

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	((4-Chlorophenyl)sulfamoyl))dimethylamine
Molecular weight formula_weight	234.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

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

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ahgH01
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	5ahgH02
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

▶

Unit-cell length a length_a	70.222 Å
Unit-cell length b length_b	71.263 Å
Unit-cell length c length_c	72.216 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.48 °
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	1.240 Å
Low-resolution limit resolution_low	43.407 Å
R factor r_factor	0.1241
R_work r_work	0.1230
R_free r_free	0.1440

Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine

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 VARIANT-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

5ahg__assembly_1__model_1

5ahg__assembly_1__model_1 | I(q)

5ahg__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Thrombin in complex with ((4-chlorophenyl)sulfamoyl))diemethylamine

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 VARIANT-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

5ahg__assembly_1__model_1

5ahg__assembly_1__model_1 | I(q)

5ahg__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

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 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)