1tbr

CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN

Method: X-RAY DIFFRACTION

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

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 6	RHODNIIN × 2 （Q06684） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	RHODNIIN × 1 （Q06684） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	RHODNIIN × 1 （Q06684） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THRB_BOVIN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain J； PDBConstruct 22–49； UniProt 318–366 Author chain L； PDBConstruct 22–49； UniProt 318–366 Author chain H； PDBConstruct 1–259； UniProt 367–625 Author chain K； PDBConstruct 1–259； UniProt 367–625

RHODNIIN

Rhodnius prolixus

UniProt Q06684

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	THROMBIN × 2 （P00735） THROMBIN × 2 （P00735） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	THROMBIN × 1 （P00735） THROMBIN × 1 （P00735） water × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	THROMBIN × 1 （P00735） THROMBIN × 1 （P00735） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THBI_RHOPR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain R； PDBConstruct 1–103； UniProt 1–103 Author chain S； PDBConstruct 1–103； UniProt 1–103

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	1tbr
Deposition date deposition_date	1995-03-03
Structure title title	CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN
Keywords keywords	COMPLEX (SERINE PROTEASE-INHIBITOR), KAZAL-TYPE INHIBITOR, THROMBIN, COMPLEX (SERINE PROTEASE-INHIBITOR) complex; COMPLEX (SERINE PROTEASE/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.

1tbr__assembly_1__model_1

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

Download this curve (.dat)

1tbr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1tbr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.35 Å
Rg (electron density)	32.83 Å
Total Rg	33.36 Å
Atom count	6838
Residues	822
Excluded volume	115140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1tbr__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1tbr__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1tbr__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	THROMBIN
Molecular weight formula_weight	5735.2 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,J
Atom count atom_count	7041

TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Entity 2 Entity 2 polymer

Description description	THROMBIN
Molecular weight formula_weight	29772.4 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,K

IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Entity 3 Entity 3 polymer

Description description	RHODNIIN
Molecular weight formula_weight	11091.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S

EGGEPCACPHALHRVCGSDGETYSNPCTLNCAKFNGKPELVKVHDGPCEPDEDEDVCQECDGDEYKPVCGSDDITYDNNCRLECASISSSPGVELKHEGPCRT

Source Source

Source organism organism	Rhodnius prolixus
NCBI taxonomy ID ncbi_taxonomy_id	13249
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	203

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1tbr.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

Domain ID domain_id	d1tbr.2
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

Domain ID domain_id	d1tbrr1
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

Domain ID domain_id	d1tbrr2
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

Domain ID domain_id	d1tbrs1
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

Domain ID domain_id	d1tbrs2
Class class	g — Small proteins
Fold Fold fold	g.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamily	g.68.1 — Kazal-type serine protease inhibitors
Family Family family	g.68.1.1 — Ovomucoid domain III-like

CATH v4.4 (10 domains)

Domain ID domain_id	1tbrH01
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	1tbrH02
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	1tbrJ00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	140 — Epsilon-Thrombin; Chain L
Homologous superfamily homologous superfamily	10 — Thrombin light chain domain

Domain ID domain_id	1tbrK01
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	1tbrK02
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	1tbrL00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	140 — Epsilon-Thrombin; Chain L
Homologous superfamily homologous superfamily	10 — Thrombin light chain domain

Domain ID domain_id	1tbrR01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1tbrR02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1tbrS01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1tbrS02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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7. Citations (7)

;Two heads are better than one: crystal structure of the insect derived double domain Kazal inhibitor rhodniin in complex with thrombin. ;

EMBO J. (1995)

PMID: 7489704 PRIMARY

A Kazal-Type Inhibitor with Thrombin Specificity from Rhodnius Prolixus

J.Biol.Chem. (1993)

;The Refined 1.9-A X-Ray Crystal Structure of D-Phe-Pro-Arg Chloromethylketone-Inhibited Human Alpha-Thrombin: Structure Analysis, Overall Structure, Electrostatic Properties, Detailed Active-Site Geometry, and Structure-Function Relationships ;

Protein Sci. (1992)

Refined Structure of the Hirudin-Thrombin Complex

J.Mol.Biol. (1991)

Crystal Structure of the Thrombin-Hirudin Complex: A Novel Mode of Serine Protease Inhibition

Embo J. (1990)

The Structure of a Complex of Recombinant Hirudin and Human Alpha-Thrombin

Science (1990)

;The Refined 1.9 A Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment ;

Embo J. (1989)

Unit-cell length a length_a	114.735 Å
Unit-cell length b length_b	112.297 Å
Unit-cell length c length_c	92.069 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1890
R_work r_work	0.1890
R_free r_free	0.2630

CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN

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

THROMBIN

State in the Current Structure

Other States of the Same Protein in the Database

RHODNIIN

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

1tbr__assembly_1__model_1

1tbr__assembly_1__model_1 | I(q)

1tbr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (7)

CRYSTAL STRUCTURE OF INSECT DERIVED DOUBLE DOMAIN KAZAL INHIBITOR RHODNIIN IN COMPLEX WITH THROMBIN

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

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

RHODNIIN

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

1tbr__assembly_1__model_1

1tbr__assembly_1__model_1 | I(q)

1tbr__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (7)