1OP0

Crystal Structure of AaV-SP-I, a Glycosylated Snake Venom Serine Proteinase from Agkistrodon acutus

PDB DOI: https://doi.org/10.2210/pdb1OP0/pdb

Classification: HYDROLASE
Organism(s): Deinagkistrodon acutus
Mutation(s): No

Deposited: 2003-03-04 Released: 2004-05-25
Deposition Author(s): Zhu, Z., Teng, M., Niu, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208
R-Value Work: 0.181
R-Value Observed: 0.181

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 26.12 kDa
Atom Count: 1,966
Modelled Residue Count: 234
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Venom serine proteinase	A	234	Deinagkistrodon acutus	Mutation(s): 0 EC: 3.4.21
UniProt
Find proteins for Q9I8X1 (Deinagkistrodon acutus) Explore Q9I8X1 Go to UniProtKB: Q9I8X1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9I8X1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.208
R-Value Work: 0.181
R-Value Observed: 0.181
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.415	α = 90
b = 74.593	β = 90
c = 82.419	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-05-25

Deposition Author(s):

Zhu, Z.

Teng, M.

Niu, L.

Revision History (Full details and data files)

Version 1.0: 2004-05-25
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

1OP0

Crystal Structure of AaV-SP-I, a Glycosylated Snake Venom Serine Proteinase from Agkistrodon acutus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)