2c4f

crystal structure of factor VII.stf complexed with pd0297121

Method: X-RAY DIFFRACTION

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

COAGULATION FACTOR VII PRECURSOR

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	TISSUE FACTOR PRECURSOR × 1 （P13726） TISSUE FACTOR PRECURSOR × 1 （P13726） CALCIUM ION × 5 2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID × 1 alpha-D-glucopyranose × 1 alpha-L-fucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA7_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain H； PDBConstruct 1–254； UniProt 213–466 Author chain L； PDBConstruct 1–142； UniProt 61–202

TISSUE FACTOR PRECURSOR

OrganismNot specified

UniProt P13726

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	COAGULATION FACTOR VII PRECURSOR × 1 （P08709） COAGULATION FACTOR VII PRECURSOR × 1 （P08709） CALCIUM ION × 5 2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID × 1 alpha-D-glucopyranose × 1 alpha-L-fucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TF_HUMAN
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain T； PDBConstruct 1–75； UniProt 38–112 Author chain U； PDBConstruct 1–116； UniProt 123–242

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	2c4f
Deposition date deposition_date	2005-10-18
Structure title title	crystal structure of factor VII.stf complexed with pd0297121
Keywords keywords	;BLOOD COAGULATION, SERINE PROTEASE, EGF, EGF-LIKE DOMAIN, GLA, RECEPTOR ENZYME, GLYCOPROTEIN, HYDROLASE, PROTEASE, HYDROXYLATION, LIPOPROTEIN, PALMITATE, TRANSMEMBRANE ;; 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.

2c4f__assembly_1__model_1

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

Download this curve (.dat)

2c4f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c4f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.37 Å
Rg (electron density)	32.63 Å
Total Rg	33.05 Å
Atom count	4730
Residues	574
Excluded volume	83849 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c4f__assembly_1__model_1`	tetrameric （4）	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 (10)

Entity 1 Entity 1 polymer

Description description	COAGULATION FACTOR VII PRECURSOR
Molecular weight formula_weight	28103.3 kDa
EC 编号 ec_number	3.4.21.21
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	5058

IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHDLSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERTLAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGYSDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMRSEPRPGVLLRAPFP

Entity 2 Entity 2 polymer

Description description	COAGULATION FACTOR VII PRECURSOR
Molecular weight formula_weight	16359.8 kDa
EC 编号 ec_number	3.4.21.21
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGSCKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSLLADGVSCTPTVEYPCGKIPILE

Entity 3 Entity 3 polymer

Description description	TISSUE FACTOR PRECURSOR
Molecular weight formula_weight	8715.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVKDVKQTYLARVFSYPA

Entity 4 Entity 4 polymer

Description description	TISSUE FACTOR PRECURSOR
Molecular weight formula_weight	13354.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

EPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVECM

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	2-{[6-{3-[AMINO(IMINO)METHYL]PHENOXY}-4-(DIISOPROPYLAMINO)-3,5-DIFLUOROPYRIDIN-2-YL]OXY}-5-[(ISOBUTYLAMINO)CARBONYL]BEN ZOIC ACID
Molecular weight formula_weight	583.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	alpha-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	alpha-L-fucopyranose
Molecular weight formula_weight	164.2 kDa
Source method src_method	man
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	328

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2c4fh1
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	d2c4fl1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d2c4fl2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.11 — EGF/Laminin
Family Family family	g.3.11.1 — EGF-type module

Domain ID domain_id	d2c4fl3
Class class	g — Small proteins
Fold Fold fold	g.32 — GLA-domain
Superfamily Superfamily superfamily	g.32.1 — GLA-domain
Family Family family	g.32.1.1 — GLA-domain

Domain ID domain_id	d2c4fu1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

CATH v4.4 (4 domains)

Domain ID domain_id	2c4fH01
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	2c4fH02
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	2c4fT00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2c4fU00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	70.993 Å
Unit-cell length b length_b	81.302 Å
Unit-cell length c length_c	125.860 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2285
R_work r_work	0.2285
R_free r_free	—

crystal structure of factor VII.stf complexed with pd0297121

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

COAGULATION FACTOR VII PRECURSOR

State in the Current Structure

Other States of the Same Protein in the Database

TISSUE FACTOR PRECURSOR

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

2c4f__assembly_1__model_1

2c4f__assembly_1__model_1 | I(q)

2c4f__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 polymer

Polymer 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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)

crystal structure of factor VII.stf complexed with pd0297121

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

COAGULATION FACTOR VII PRECURSOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TISSUE FACTOR PRECURSOR

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

2c4f__assembly_1__model_1

2c4f__assembly_1__model_1 | I(q)

2c4f__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 polymer

Polymer 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) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

7. Citations (1)