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- PDB-6ugy: Crystal structure of the Fc fragment of anti-TNFa antibody inflix... -

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Basic information

Entry
Database: PDB / ID: 6ugy
TitleCrystal structure of the Fc fragment of anti-TNFa antibody infliximab (Remicade) in a primative orthorhombic crystal form, Lot C
ComponentsRemicade Fc
KeywordsIMMUNE SYSTEM / Antibody / biologic / biosimilar / infliximab / Remicade / fragment crystallizable
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMayclin, S.J. / Edwards, T.E.
CitationJournal: BioDrugs / Year: 2020
Title: Crystal Structures of PF-06438179/GP1111, an Infliximab Biosimilar.
Authors: Lerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Zou, Q. / Conlon, H.D.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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

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Assembly

Deposited unit
A: Remicade Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0396
Polymers28,3611
Non-polymers1,6785
Water2,522140
1
A: Remicade Fc
hetero molecules

A: Remicade Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,07812
Polymers56,7232
Non-polymers3,35510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area7700 Å2
ΔGint-75 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.340, 148.650, 75.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

ZN

21A-657-

HOH

31A-715-

HOH

41A-736-

HOH

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Components

#1: Protein Remicade Fc / Immunoglobulin gamma-1 heavy chain NIE


Mass: 28361.252 Da / Num. of mol.: 1 / Fragment: LotC_Fc
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL protein with JCSG+ E7 Opt screen H2 (267146h2): 4% 2-propanol, 200 mM zinc acetate, 100 mM sodium cacodylate, pH 6.8, cryoprotectant: 20% ethylene glycol, puckID kux1-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 5, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17056 / % possible obs: 99.9 % / Redundancy: 6.101 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.094 / Χ2: 0.988 / Net I/σ(I): 15.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.180.5583.2812140.8710.61100
2.15-2.216.2050.4544.0212150.9080.49699.9
2.21-2.286.2120.4154.4211840.9040.454100
2.28-2.356.1780.3315.2911380.9620.362100
2.35-2.426.20.2986.0511200.950.325100
2.42-2.516.2120.2547.0410750.9640.277100
2.51-2.66.1890.2068.3510520.9820.226100
2.6-2.716.1470.17510.039970.9810.192100
2.71-2.836.1640.14211.959550.9880.155100
2.83-2.976.1810.11414.849260.9930.125100
2.97-3.136.1550.08718.038890.9950.095100
3.13-3.326.1020.06622.248310.9970.073100
3.32-3.556.0810.05727.037920.9980.062100
3.55-3.836.0480.05128.857360.9980.056100
3.83-4.26.0220.04433.216870.9990.04899.9
4.2-4.75.9840.03836.646140.9990.041100
4.7-5.425.8680.03635.965540.9990.0499.8
5.42-6.645.80.0435.474760.9990.044100
6.64-9.395.5040.03538.113790.9990.039100
9.39-504.6620.03437.242220.9990.03896.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4CDH

4cdh


Resolution: 2.1→50 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.87
RfactorNum. reflection% reflection
Rfree0.2283 852 5 %
Rwork0.1785 --
obs0.181 17047 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.49 Å2 / Biso mean: 44.1507 Å2 / Biso min: 12.64 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 103 140 1856
Biso mean--67.51 39.27 -
Num. residues----206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081777
X-RAY DIFFRACTIONf_angle_d0.922436
X-RAY DIFFRACTIONf_chiral_restr0.054294
X-RAY DIFFRACTIONf_plane_restr0.005298
X-RAY DIFFRACTIONf_dihedral_angle_d16.8031077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.23160.30971380.21572630
2.2316-2.40380.28331410.20422664
2.4038-2.64570.231400.19392679
2.6457-3.02840.25011420.19612693
3.0284-3.81510.24091430.17572713
3.8151-500.18131480.15432816
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)
11.06750.86110.07161.94170.78270.8547-0.0521-0.77581.32030.4180.203-0.1583-0.303-0.05660.40670.3769-0.0055-0.08310.3552-0.39380.76047.896325.0421-5.4426
22.38220.4058-0.2691.2064-0.08331.1296-0.0288-0.5809-0.86160.1021-0.0399-0.06630.0790.1723-0.0050.21480.0148-0.0050.3050.14010.284519.4184-5.8014-12.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 241 through 339 )A241 - 339
2X-RAY DIFFRACTION2chain 'A' and (resid 340 through 446 )A340 - 446

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