2e3x

Crystal structure of Russell's viper venom metalloproteinase

Method: X-RAY DIFFRACTION

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

Coagulation factor X-activating enzyme heavy chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
3	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RVVX_DABRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–427； UniProt 1–429

Coagulation factor X-activating enzyme light chain 2

OrganismNot specified

UniProt Q4PRD2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
3	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 1 × 1 （Q4PRD1） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LC2_DABRU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–134； UniProt 25–158

Coagulation factor X-activating enzyme light chain 1

OrganismNot specified

UniProt Q4PRD1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count
3	Other combination	Heteromer	Protein 3 其他Polymer 2	Coagulation factor X-activating enzyme heavy chain × 1 （Q7LZ61） Coagulation factor X-activating enzyme light chain 2 × 1 （Q4PRD2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZINC ION × 1 CALCIUM ION × 5 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LC1_DABRU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–122； UniProt 25–146

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	2e3x
Deposition date deposition_date	2006-11-30
Structure title title	Crystal structure of Russell's viper venom metalloproteinase
Keywords keywords	disintegrin, metalloproteinase, C-type lectin, HYDROLASE, BLOOD CLOTTING, TOXIN; HYDROLASE, BLOOD CLOTTING, TOXIN
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.

2e3x__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2e3x__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2e3x__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	29.81 Å
Rg (electron density)	28.83 Å
Total Rg	29.61 Å
Atom count	5438
Residues	665
Excluded volume	95966 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2e3x__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2e3x__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2e3x__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 (9)

Entity 1 Entity 1 polymer

Description description	Coagulation factor X-activating enzyme heavy chain
Molecular weight formula_weight	47703.1 kDa
EC 编号 ec_number	3.4.24.58
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	5438

LVSTSAQFNKIFIELVIIVDHSMAKKCNSTATNTKIYEIVNSANEIFNPLNIHVTLIGVEFWCDRDLINVTSSADETLNSFGEWRASDLMTRKSHDNALLFTDMRFDLNTLGITFLAGMCQAYRSVGIVQEQGNRNFKTAVIMAHELSHNLGMYHDGKNCICNDSSCVMSPVLSDQPSKLFSNCSIHDYQRYLTRYKPKCIFNPPLRKDIVSPPVCGNEIWEEGEECDCGSPANCQNPCCDAATCKLKPGAECGNGLCCYQCKIKTAGTVCRRARDECDVPEHCTGQSAECPRDQLQQNGKPCQNNRGYCYNGDCPIMRNQCISLFGSRANVAKDSCFQENLKGSYYGYCRKENGRKIPCAPQDVKCGRLFCLNNSPRNKNPCNMHYSCMDQHKGMVDPGTKCEDGKVCNNKRQCVDVNTAYQSTTG

Entity 2 Entity 2 polymer

Description description	Coagulation factor X-activating enzyme light chain 2
Molecular weight formula_weight	15961.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LDCPPDSSLYRYFCYRVFKEHKTWEAAERFCMEHPNNGHLVSIESMEEAEFVAKLLSNTTGKFITHFWIGLMIKDKEQECSSEWSDGSSVSYDKLGKQEFRKCFVLEKESGYRMWFNRNCEERYLFVCKVPPEC

Entity 3 Entity 3 polymer

Description description	Coagulation factor X-activating enzyme light chain 1
Molecular weight formula_weight	14357.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

LDCPSGWLSYEQHCYKGFNDLKNWTDAEKFCTEQKKGSHLVSLHSREEEKFVVNLISENLEYPATWIGLGNMWKDCRMEWSDRGNVKYKALAEESYCLIMITHEKVWKSMTCNFIAPVVCKF

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 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	2

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
Molecular weight formula_weight	388.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2e3xb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

Domain ID domain_id	d2e3xc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2e3xA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	2e3xB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	2e3xC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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Unit-cell length a length_a	70.350 Å
Unit-cell length b length_b	91.730 Å
Unit-cell length c length_c	152.930 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	2.910 Å
Low-resolution limit resolution_low	44.600 Å
R factor r_factor	—
R_work r_work	0.2180
R_free r_free	0.2730

Crystal structure of Russell's viper venom metalloproteinase

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

Coagulation factor X-activating enzyme heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Coagulation factor X-activating enzyme light chain 2

State in the Current Structure

Other States of the Same Protein in the Database

Coagulation factor X-activating enzyme light chain 1

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

2e3x__assembly_2__model_1

2e3x__assembly_2__model_1 | I(q)

2e3x__assembly_2__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 (9)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of Russell's viper venom metalloproteinase

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

Coagulation factor X-activating enzyme 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

Coagulation factor X-activating enzyme light chain 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Coagulation factor X-activating enzyme light chain 1

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

2e3x__assembly_2__model_1

2e3x__assembly_2__model_1 | I(q)

2e3x__assembly_2__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 (9)

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 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)