SAXSdb — 1b5g

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

ALPHA-THROMBIN

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	HIRUGEN × 1 （P09945） ;[[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium ; × 1 SODIUM ION × 2 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 1–36； UniProt 328–363 Author chain H； PDBConstruct 1–259； UniProt 364–622

HIRUGEN

OrganismNot specified

UniProt P09945

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	ALPHA-THROMBIN × 1 （P00734） ALPHA-THROMBIN × 1 （P00734） ;[[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium ; × 1 SODIUM ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITH3_HIRME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–12； UniProt 60–71

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	1b5g
Deposition date deposition_date	1998-03-05
Structure title title	HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN
Keywords keywords	SERINE PROTEASE-INHIBITOR, 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.

1b5g__assembly_1__model_1

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

Download this curve (.dat)

1b5g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1b5g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.12 Å
Rg (electron density)	17.92 Å
Total Rg	18.94 Å
Atom count	2393
Residues	288
Excluded volume	42457 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1b5g__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 (6)

Entity 1 Entity 1 polymer

Description description	ALPHA-THROMBIN
Molecular weight formula_weight	4096.5 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
Atom count atom_count	2526

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 Entity 2 polymer

Description description	ALPHA-THROMBIN
Molecular weight formula_weight	29780.2 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

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 Entity 3 polymer

Description description	HIRUGEN
Molecular weight formula_weight	1534.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

NGDFEEIPEEYL

Entity 4 Entity 4 non-polymer

Description description	;[[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium ;
Molecular weight formula_weight	564.7 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	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b5g.1
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (2 domains)

Domain ID domain_id	1b5gH01
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	1b5gH02
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	70.840 Å
Unit-cell length b length_b	72.080 Å
Unit-cell length c length_c	73.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.90 °
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	2.070 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	—
R_work r_work	0.1640
R_free r_free	—

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

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

ALPHA-THROMBIN

State in the Current Structure

Other States of the Same Protein in the Database

HIRUGEN

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

1b5g__assembly_1__model_1

1b5g__assembly_1__model_1 | I(q)

1b5g__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (3)

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

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

ALPHA-THROMBIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIRUGEN

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

1b5g__assembly_1__model_1

1b5g__assembly_1__model_1 | I(q)

1b5g__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (3)