SAXSdb — 3kqd

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

factor Xa heavy chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE ; × 1 SODIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FA10_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 235–468 Author chain L； PDBConstruct 1–52； UniProt 127–178

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	3kqd
Deposition date deposition_date	2009-11-17
Structure title title	Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one
Keywords keywords	;GLYCOPROTEIN, SERINE PROTEASE, PLASMA, BLOOD COAGULATION FACTOR, PROTEIN INHIBITOR COMPLEX, CALCIUM- BINDING, BLOOD COAGULATION, CALCIUM, PROTEASE, SECRETED, EGF-like domain, Gamma-carboxyglutamic acid, HYDROLASE ;; 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.

3kqd__assembly_1__model_1

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

Download this curve (.dat)

3kqd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kqd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.64 Å
Rg (electron density)	18.48 Å
Total Rg	19.51 Å
Atom count	2266
Residues	286
Excluded volume	40009 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kqd__assembly_1__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	factor Xa heavy chain
Molecular weight formula_weight	26447.1 kDa
EC 编号 ec_number	3.4.21.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2282

IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTEQEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLMTQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDACQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKT

Entity 2 Entity 2 polymer

Description description	factor Xa light chain
Molecular weight formula_weight	5589.2 kDa
EC 编号 ec_number	3.4.21.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

KLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACIPTGPYPCGKQTLE

Entity 3 Entity 3 non-polymer

Description description	;1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE ;
Molecular weight formula_weight	599.6 kDa
Source method src_method	syn
Copy count entity_count	1

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3kqda_
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	d3kqdl_
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

CATH v4.4 (3 domains)

Domain ID domain_id	3kqdA01
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	3kqdA02
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	3kqdL00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	10 — Laminin

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Unit-cell length a length_a	57.700 Å
Unit-cell length b length_b	72.100 Å
Unit-cell length c length_c	76.800 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	2.750 Å
Low-resolution limit resolution_low	38.400 Å
R factor r_factor	0.1950
R_work r_work	0.1870
R_free r_free	0.2540

Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one

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

factor Xa heavy chain

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

3kqd__assembly_1__model_1

3kqd__assembly_1__model_1 | I(q)

3kqd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one

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

factor Xa 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3kqd__assembly_1__model_1

3kqd__assembly_1__model_1 | I(q)

3kqd__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)