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- PDB-5nb5: Principles for computational design of antibodies -

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Basic information

Entry
Database: PDB / ID: 5nb5
TitlePrinciples for computational design of antibodies
Components(design of antibodies) x 2
KeywordsIMMUNE SYSTEM / antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDym, O. / Fleishman, S.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Principles for computational design of binding antibodies.
Authors: Baran, D. / Pszolla, M.G. / Lapidoth, G.D. / Norn, C. / Dym, O. / Unger, T. / Albeck, S. / Tyka, M.D. / Fleishman, S.J.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 12, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: design of antibodies
H: design of antibodies
M: design of antibodies
I: design of antibodies


Theoretical massNumber of molelcules
Total (without water)95,0584
Polymers95,0584
Non-polymers00
Water00
1
L: design of antibodies
H: design of antibodies


Theoretical massNumber of molelcules
Total (without water)47,5292
Polymers47,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area19780 Å2
MethodPISA
2
M: design of antibodies
I: design of antibodies


Theoretical massNumber of molelcules
Total (without water)47,5292
Polymers47,5292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 109.390, 158.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21M
12H
22I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPCYSCYSLA1 - 2181 - 218
21ASPASPCYSCYSMC1 - 2181 - 218
12GLNGLNLYSLYSHB1 - 2171 - 217
22GLNGLNLYSLYSID1 - 2171 - 217

NCS ensembles :
ID
1
2

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Components

#1: Antibody design of antibodies


Mass: 24056.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Antibody design of antibodies


Mass: 23472.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 2.9 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M (NH4)2SO4 0.05M Tris pH=8.5 12.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 3→90 Å / Num. obs: 21280 / % possible obs: 93 % / Redundancy: 4.2 % / Rsym value: 0.195 / Net I/σ(I): 3.8
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2854 / % possible all: 85.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQ9, 2HFF

3qq9

2hff


Resolution: 3→90 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.844 / SU B: 48.33 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25732 1105 5 %RANDOM
Rwork0.22347 ---
obs0.22521 20906 96.53 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso mean: 51.253 Å2
Baniso -1Baniso -2Baniso -3
1--3.41 Å2-0 Å20 Å2
2--2.61 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 3→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 0 0 6558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.026758
X-RAY DIFFRACTIONr_bond_other_d0.0020.025992
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9419192
X-RAY DIFFRACTIONr_angle_other_deg0.931313998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8725858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90924.06266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2251530
X-RAY DIFFRACTIONr_chiral_restr0.080.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021366
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_it1.3442.3843450
X-RAY DIFFRACTIONr_mcbond_other1.3442.3833449
X-RAY DIFFRACTIONr_mcangle_it2.3913.5654302
X-RAY DIFFRACTIONr_mcangle_other2.3913.5664303
X-RAY DIFFRACTIONr_scbond_it1.2162.4773308
X-RAY DIFFRACTIONr_scbond_other1.2162.4773309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1163.6594891
X-RAY DIFFRACTIONr_long_range_B_refined5.4444.63826201
X-RAY DIFFRACTIONr_long_range_B_other5.4444.63926202
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 / Rms dev position: 0.09 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11L13136
12M13136
21H12148
22I12148
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 74 -
Rwork0.342 1472 -
obs--94.85 %
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)
10.50470.0769-0.25183.5695-0.06480.2444-0.0301-0.08970.03730.3368-0.05470.0384-0.16150.07560.08470.3479-0.022-0.10840.0320.03530.12526.81695.93916.47
22.07910.98220.37432.57280.10651.8514-0.07080.03290.24240.10640.00570.1109-0.35480.11080.06510.21090.003-0.05020.01820.00780.052-2.304104.8474.132
31.4934-0.73650.40983.0991-1.08231.61560.12560.3440.1143-0.6387-0.1052-0.40540.23930.1982-0.02040.49610.05730.09710.1935-0.0160.136-12.246108.49442.298
41.8249-0.49890.08692.3783-0.39142.7816-0.00250.0409-0.2294-0.09320.09990.11560.5749-0.1505-0.09740.3553-0.01980.02710.053-0.04950.1129-19.93107.18258.012
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 218
2X-RAY DIFFRACTION2H1 - 217
3X-RAY DIFFRACTION3M1 - 218
4X-RAY DIFFRACTION4I1 - 217

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