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- PDB-5n7w: Computationally designed functional antibody -

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Basic information

Entry
Database: PDB / ID: 5n7w
TitleComputationally designed functional antibody
Components
  • Antibody Fragment Heavy Chain
  • Antibody Fragment Light Chain
  • Interleukin-17A
KeywordsIMMUNE SYSTEM / Computationally designed antibody IL17
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / positive regulation of chemokine (C-X-C motif) ligand 1 production / cell death / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of osteoclast differentiation / keratinocyte proliferation / defense response to fungus / cellular response to interleukin-1 / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHargreaves, D. / Breed, J.
CitationJournal: Cell Rep / Year: 2018
Title: Computational Design of Epitope-Specific Functional Antibodies.
Authors: Nimrod, G. / Fischman, S. / Austin, M. / Herman, A. / Keyes, F. / Leiderman, O. / Hargreaves, D. / Strajbl, M. / Breed, J. / Klompus, S. / Minton, K. / Spooner, J. / Buchanan, A. / Vaughan, T.J. / Ofran, Y.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody Fragment Heavy Chain
B: Antibody Fragment Light Chain
H: Antibody Fragment Heavy Chain
L: Antibody Fragment Light Chain
X: Interleukin-17A
Y: Interleukin-17A


Theoretical massNumber of molelcules
Total (without water)129,6266
Polymers129,6266
Non-polymers00
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15480 Å2
ΔGint-101 kcal/mol
Surface area48960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.240, 199.980, 76.350
Angle α, β, γ (deg.)90.00, 96.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21H
12B
22L
13X
23Y

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 220
2010H1 - 220
1020B1 - 209
2020L1 - 209
1030X10 - 125
2030Y10 - 125

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Antibody Fragment Heavy Chain /


Mass: 23885.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Antibody Fragment Light Chain /


Mass: 23399.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Interleukin-17A / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 17528.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q16552
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 18% (w/v) PEG-MME 2000, 100mM PCTP pH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.96→75.87 Å / Num. obs: 86657 / % possible obs: 96.5 % / Redundancy: 3.1 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4969 / CC1/2: 0.587 / % possible all: 74.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→75.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.898 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24974 4249 4.9 %RANDOM
Rwork0.19905 ---
obs0.20151 82363 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.525 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å2-0.15 Å2
2---2.67 Å20 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.96→75.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8244 0 0 678 8922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.028485
X-RAY DIFFRACTIONr_bond_other_d0.0060.027724
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.94111582
X-RAY DIFFRACTIONr_angle_other_deg1.39317885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38951061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3724.077336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.653151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.881534
X-RAY DIFFRACTIONr_chiral_restr0.1170.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219542
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021914
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.765.1134271
X-RAY DIFFRACTIONr_mcbond_other4.7595.1124270
X-RAY DIFFRACTIONr_mcangle_it6.7417.6445323
X-RAY DIFFRACTIONr_mcangle_other6.747.6455324
X-RAY DIFFRACTIONr_scbond_it5.0475.4114214
X-RAY DIFFRACTIONr_scbond_other5.0465.4124215
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3157.9616260
X-RAY DIFFRACTIONr_long_range_B_refined10.1440.4279478
X-RAY DIFFRACTIONr_long_range_B_other10.1440.4319479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A225320.08
12H225320.08
21B218400.12
22L218400.12
31X100920.12
32Y100920.12
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 254 -
Rwork0.366 4714 -
obs--74.07 %

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