2E3X | pdb_00002e3x

Crystal structure of Russell's viper venom metalloproteinase

PDB DOI: https://doi.org/10.2210/pdb2E3X/pdb

Classification: HYDROLASE, BLOOD CLOTTING, TOXIN
Organism(s): Daboia siamensis
Mutation(s): No

Deposited: 2006-11-30 Released: 2007-12-11
Deposition Author(s): Igarashi, T., Takeda, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.273 (Depositor), 0.270 (DCC)
R-Value Work:
0.218 (Depositor), 0.222 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Crystal structure of RVV-X: an example of evolutionary gain of specificity by ADAM proteinases.

Takeda, S., Igarashi, T., Mori, H.

(2007) FEBS Lett 581: 5859-5864

PubMed: 18060879 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2007.11.062
Primary Citation Related Structures:
2E3X

PubMed Abstract:
Russell's viper venom factor X activator (RVV-X) is a heterotrimeric metalloproteinase with a mammalian ADAM-like heavy chain and two lectin-like light chains. The crystal structure of RVV-X has been determined at 2.9 A resolution and shows a hook-spanner-wrench-like architecture, in which the metalloproteinase/disintegrin region constitutes a hook, and the lectin-like domains constitute a handle. A 6.5nm separation between the catalytic site and a putative exosite suggests a docking model for factor X. The structure provides a typical example of the molecular evolution of multi-subunit proteins and insights into the molecular basis of target recognition and proteolysis by ADAM/adamalysin/reprolysin proteinases.

Organizational Affiliation

Department of Cardiac Physiology, National Cardiovascular Center Research Institute, 5-7-1 Fujishiro-dai, Suita, Osaka 565-8565, Japan. stakeda@ri.ncvc.go.jp

Macromolecule Content

Total Structure Weight: 80.29 kDa
Atom Count: 5,438
Modeled Residue Count: 665
Deposited Residue Count: 683
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X-activating enzyme heavy chain	A	427	Daboia siamensis	Mutation(s): 0 EC: 3.4.24.58
UniProt
Find proteins for Q7LZ61 (Daboia siamensis) Explore Q7LZ61 Go to UniProtKB: Q7LZ61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7LZ61
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X-activating enzyme light chain 2	B	134	Daboia siamensis	Mutation(s): 0
UniProt
Find proteins for Q4PRD2 (Daboia siamensis) Explore Q4PRD2 Go to UniProtKB: Q4PRD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4PRD2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X-activating enzyme light chain 1	C	122	Daboia siamensis	Mutation(s): 0
UniProt
Find proteins for Q4PRD1 (Daboia siamensis) Explore Q4PRD1 Go to UniProtKB: Q4PRD1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4PRD1
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G04854NQ GlyCosmos: G04854NQ GlyGen: G04854NQ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GM6 Query on GM6 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE C₂₀ H₂₈ N₄ O₄ NITYDPDXAAFEIT-DYVFJYSZSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain F [auth A]	F [auth A], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A], K [auth A], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.273 (Depositor), 0.270 (DCC)
R-Value Work: 0.218 (Depositor), 0.222 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.35	α = 90
b = 91.73	β = 90
c = 152.93	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-12-11

Deposition Author(s):

Igarashi, T.

Takeda, S.

Revision History (Full details and data files)

Version 1.0: 2007-12-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 2.0: 2019-12-25
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 3.2: 2024-10-23
Changes: Structure summary