2E3X
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 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.273 
- R-Value Work: 0.218 
This is version 3.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Coagulation factor X-activating enzyme heavy chain | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q7LZ61 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Coagulation factor X-activating enzyme light chain 2 | 134 | Daboia siamensis | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q4PRD2 (Daboia siamensis) Explore Q4PRD2  Go to UniProtKB:  Q4PRD2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q4PRD2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Coagulation factor X-activating enzyme light chain 1 | 122 | Daboia siamensis | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q4PRD1 (Daboia siamensis) Explore Q4PRD1  Go to UniProtKB:  Q4PRD1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q4PRD1 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D 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 | ||
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 | L [auth A] | 3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE C20 H28 N4 O4 NITYDPDXAAFEIT-DYVFJYSZSA-N | |||
NAG Query on NAG | F [auth A], M [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | G [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | H [auth A], I [auth A], J [auth A], K [auth A], N [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.91 Å
- R-Value Free: 0.273 
- R-Value Work: 0.218 
- 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 Name | Purpose |
---|---|
ADSC | data collection |
MOLREP | phasing |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
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