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- PDB-7qaj: ZK002 with Anti-angiogenic and Anti-inflamamtory Properties -

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Basic information

Entry
Database: PDB / ID: 7qaj
TitleZK002 with Anti-angiogenic and Anti-inflamamtory Properties
Components
  • Snaclec clone 2100755 alpha
  • Snaclec clone 2100755 beta
KeywordsPEPTIDE BINDING PROTEIN / antiangiogenic activity
Function / homology
Function and homology information


venom-mediated disruption of cell wall in another organism / oligosaccharide binding / peptidoglycan binding / response to peptide hormone / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / : / toxin activity / positive regulation of cell population proliferation / extracellular space
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Snaclec clone 2100755
Similarity search - Component
Biological speciesDeinagkistrodon acutus (Chinese moccasin)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWong, W.Y. / Chan, B.D. / Muk Lan Lee, M. / Dai, X. / Tsim, K.W.K. / Hsiao, W.L.W. / Li, M. / Li, X.Y. / Tai, W.C.S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Front Pharmacol / Year: 2023
Title: Isolation and characterization of ZK002, a novel dual function snake venom protein from Deinagkistrodon acutus with anti-angiogenic and anti-inflammatory properties.
Authors: Chan, B.D. / Wong, W.Y. / Lee, M.M. / Yue, P.Y. / Dai, X. / Tsim, K.W. / Hsiao, W.W. / Li, M. / Li, X.Y. / Tai, W.C.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Snaclec clone 2100755 beta
D: Snaclec clone 2100755 beta
F: Snaclec clone 2100755 beta
H: Snaclec clone 2100755 beta
C: Snaclec clone 2100755 alpha
A: Snaclec clone 2100755 alpha
G: Snaclec clone 2100755 alpha
E: Snaclec clone 2100755 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,33314
Polymers123,7568
Non-polymers5766
Water9,908550
1
B: Snaclec clone 2100755 beta
A: Snaclec clone 2100755 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0353
Polymers30,9392
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Snaclec clone 2100755 beta
C: Snaclec clone 2100755 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2275
Polymers30,9392
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Snaclec clone 2100755 beta
E: Snaclec clone 2100755 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1314
Polymers30,9392
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: Snaclec clone 2100755 beta
G: Snaclec clone 2100755 alpha


Theoretical massNumber of molelcules
Total (without water)30,9392
Polymers30,9392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.160, 54.290, 107.640
Angle α, β, γ (deg.)90.000, 100.560, 90.000
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Snaclec clone 2100755 beta / C-type lectin clone 2100755 / beta subunit of ZK002


Mass: 15550.368 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The beta subunit of ZK002
Source: (gene. exp.) Deinagkistrodon acutus (Chinese moccasin)
Production host: Deinagkistrodon acutus (Chinese moccasin) / References: UniProt: Q8JIV8
#2: Protein
Snaclec clone 2100755 alpha


Mass: 15388.710 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The alpha subunit of ZK002
Source: (gene. exp.) Deinagkistrodon acutus (Chinese moccasin)
Production host: Deinagkistrodon acutus (Chinese moccasin)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M (NH4)2SO4 0.1M Bis Tris pH=6 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.1→27.45 Å / Num. obs: 68733 / % possible obs: 98.1 % / Redundancy: 10.7 % / CC1/2: 0.75 / Net I/σ(I): 41.05
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.19 % / Num. unique obs: 6489 / CC1/2: 0.735 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WT9

1wt9


Resolution: 2.1→24.45 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 3269 4.83 %
Rwork0.198 64391 -
obs0.2 67660 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.89 Å2 / Biso mean: 38.52 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 2.1→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 0 30 550 8893
Biso mean--67.03 34.79 -
Num. residues----1030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13130.28831210.251268595
2.1313-2.16460.30181380.2449273095
2.1646-2.20010.32661460.2381267596
2.2001-2.23810.28721510.233268595
2.2381-2.27870.29061640.2302268795
2.2787-2.32260.29681300.2242271096
2.3226-2.370.27971300.2181275997
2.37-2.42150.29621390.2247272197
2.4215-2.47780.27831380.2192277397
2.4778-2.53970.31661210.2277279698
2.5397-2.60840.31661590.2313276199
2.6084-2.68510.29541550.2342280999
2.6851-2.77180.30051460.2365282699
2.7718-2.87080.34551230.25012880100
2.8708-2.98570.27421380.23072831100
2.9857-3.12150.29221250.22132870100
3.1215-3.28590.23411280.21882843100
3.2859-3.49160.21591760.19162845100
3.4916-3.76090.21031560.17322876100
3.7609-4.13890.2011630.15942849100
4.1389-4.73660.15811420.13612876100
4.7366-5.96290.17091260.14932936100
5.9629-24.450.21131540.1825296899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.01920.8065-1.5922.0813-0.08572.7081-0.05530.01030.15290.20630.02110.33050.1372-0.10530.03550.16830.0024-0.00910.12330.00180.20626.1034-8.583957.8123
21.4777-0.25120.00381.2112-0.20755.67980.0128-0.1333-0.04030.14580.0407-0.1639-0.19790.6438-0.03860.1696-0.0162-0.01180.1787-0.03850.250919.0519-33.66858.3251
31.84940.2949-1.43280.93450.83183.09180.04470.4252-0.1969-0.15420.0071-0.0477-0.6715-1.4318-0.00260.2610.1345-0.04230.5413-0.01340.199326.2347-26.5338-12.5951
44.5591-1.1346-1.97292.423-0.67353.2742-0.0221-0.31130.4637-0.1832-0.0069-0.5346-0.10840.55030.01410.33480.00830.05130.4357-0.01770.376338.0942-1.8523-7.7737
51.3481-0.83480.81841.4441-1.86862.90930.06380.186-0.0108-0.14430.06240.04370.1186-0.2522-0.1420.1984-0.0383-0.00680.21-0.02140.16734.2592-27.22434.922
62.60751.277-2.06872.4662-0.80822.7382-0.4894-0.0727-0.3437-0.41750.0987-0.52880.36160.44310.15060.2349-0.03870.10240.2882-0.00510.263730.4011-8.762743.856
72.4924-1.5076-1.3123.44480.13463.1024-0.4404-0.4543-0.06690.58710.50.55060.07030.0077-0.06970.36010.16920.12070.39420.07780.306814.4391-4.93846.4322
82.24180.9165-0.22620.60840.3154.12990.2027-0.4272-0.15090.0888-0.0788-0.14550.08270.4789-0.12090.20930.0477-0.04660.41950.02610.221440.2659-24.951611.4246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN B AND RESSEQ 0:124)B0 - 124
2X-RAY DIFFRACTION2(CHAIN D AND RESSEQ 0:124)D0 - 124
3X-RAY DIFFRACTION3(CHAIN F AND RESSEQ 0:123)F0 - 123
4X-RAY DIFFRACTION4(CHAIN H AND RESSEQ 1:124)H1 - 124
5X-RAY DIFFRACTION5(CHAIN C AND RESSEQ 2:134)C2 - 134
6X-RAY DIFFRACTION6(CHAIN A AND RESSEQ 2:134)A2 - 134
7X-RAY DIFFRACTION7(CHAIN G AND RESSEQ 2:134)G2 - 134
8X-RAY DIFFRACTION8(CHAIN E AND RESSEQ 2:134)E2 - 134

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