1toc

STRUCTURE OF SERINE PROTEINASE

Method: X-RAY DIFFRACTION

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

THROMBIN

Bos taurus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	ORNITHODORIN × 1 （P56409） water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	ORNITHODORIN × 1 （P56409） water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	ORNITHODORIN × 1 （P56409） water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 3	ORNITHODORIN × 1 （P56409） water × 1	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 A； PDBConstruct 1–49； UniProt 318–366 Author chain C； PDBConstruct 1–49； UniProt 318–366 Author chain E； PDBConstruct 1–49； UniProt 318–366 Author chain G； PDBConstruct 1–49； UniProt 318–366 Author chain B； PDBConstruct 1–259； UniProt 367–625 Author chain D； PDBConstruct 1–259； UniProt 367–625 Author chain F； PDBConstruct 1–259； UniProt 367–625 Author chain H； PDBConstruct 1–259； UniProt 367–625

ORNITHODORIN

Ornithodoros moubata

UniProt P56409

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORNT_ORNMO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain R； PDBConstruct 1–120； UniProt 1–119 Author chain S； PDBConstruct 1–120； UniProt 1–119 Author chain T； PDBConstruct 1–120； UniProt 1–119 Author chain U； PDBConstruct 1–120； UniProt 1–119

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	1toc
Deposition date deposition_date	1996-07-20
Structure title title	STRUCTURE OF SERINE PROTEINASE
Keywords keywords	;VITAMIN K, ZYMOGEN, GAMMA-CARBOXYGLUTAMIC ACID, ACUTE PHASE, LIVER, HYDROLASE, SERINE PROTEASE KUNITZ-LIKE INHIBITOR, KRINGLE, COMPLEX (HYDROLASE-INHIBITOR) COMPLEX ;; COMPLEX (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.

1toc__assembly_1__model_1

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

Download this curve (.dat)

1toc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1toc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.94 Å
Rg (electron density)	21.80 Å
Total Rg	22.71 Å
Atom count	3359
Residues	407
Excluded volume	56580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1toc__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1toc__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1toc__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1toc__assembly_4__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	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	13467

TSEDHFQPFFNEKTFGAGEADCGLRPLFEKKQVQDQTEKELFESYIEGR

Source Source

Source organism organism	Bos taurus
Common name common_name	cattle
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

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	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

IVEGQDAEVGLSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTVDDLLVRIGKHSRTRYERKVEKISMLDKIYIHPRYNWKENLDRDIALLKLKRPIELSDYIHPVCLPDKQTAAKLLHAGFKGRVTGWGNRRETWTTSVAEVQPSVLQVVNLPLVERPVCKASTRIRITDNMFCAGYKPGEGKRGDACEGDSGGPFVMKSPYNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDRLGS

Source Source

Source organism organism	Bos taurus
Common name common_name	cattle
NCBI taxonomy ID ncbi_taxonomy_id	9913
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	ORNITHODORIN
Molecular weight formula_weight	12726.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SLNVLCNNPHTADCNNDAQVDRYFREGTTCLMSPACTSEGYASQHECQQACFVGGEDHSSEMHSSCLGDPPTSCAEGTDITYYDSDSKTCKVLAASCPSGENTFESEVECQVACGAPIEG

Source Source

Source organism organism	Ornithodoros moubata
NCBI taxonomy ID ncbi_taxonomy_id	6938
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	31

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1toc.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	d1toc.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	d1toc.3
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	d1toc.4
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	d1tocr1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1tocr2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1tocs1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1tocs2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1toct1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1toct2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1tocu1
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

Domain ID domain_id	d1tocu2
Class class	g — Small proteins
Fold Fold fold	g.8 — BPTI-like
Superfamily Superfamily superfamily	g.8.1 — BPTI-like
Family Family family	g.8.1.2 — Soft tick anticoagulant proteins

CATH v4.4 (16 domains)

Domain ID domain_id	1tocB01
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	1tocB02
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	1tocD01
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	1tocD02
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	1tocF01
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	1tocF02
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	1tocH01
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	1tocH02
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	1tocR01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocR02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocS01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocS02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocT01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocT02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocU01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

Domain ID domain_id	1tocU02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily	10 — Pancreatic trypsin inhibitor Kunitz domain

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Unit-cell length a length_a	125.300 Å
Unit-cell length b length_b	89.900 Å
Unit-cell length c length_c	101.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	—

STRUCTURE OF SERINE PROTEINASE

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

ORNITHODORIN

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

1toc__assembly_1__model_1

1toc__assembly_1__model_1 | I(q)

1toc__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. Citations (3)

STRUCTURE OF SERINE PROTEINASE

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

ORNITHODORIN

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

1toc__assembly_1__model_1

1toc__assembly_1__model_1 | I(q)

1toc__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. Citations (3)