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- PDB-6ugx: Crystal structure of the Fc fragment of PF06438179/GP1111 an infl... -

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Basic information

Entry
Database: PDB / ID: 6ugx
TitleCrystal structure of the Fc fragment of PF06438179/GP1111 an infliximab biosimilar in a primative orthorhombic crystal form, Lot A
ComponentsPF-06438179/GP1111 Fc
KeywordsIMMUNE SYSTEM / Antibody / biologic / biosimilar / infliximab / fragment crystallizable
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / 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_validate_close_contact / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_validate_close_contact.auth_asym_id_2 / _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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PF-06438179/GP1111 Fc
B: PF-06438179/GP1111 Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5216
Polymers56,7232
Non-polymers2,7984
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint54 kcal/mol
Surface area20930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.400, 74.610, 149.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PF-06438179/GP1111 Fc


Mass: 28361.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Mus musculus (house mouse) / References: UniProt: P0DOX5

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...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: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 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]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 341 molecules

#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL protein with 200 mM potassium nitrate, 20% PEG3350, cryoprotectant: 20% ethylene glycol, puckID sxt1-6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 22, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32975 / % possible obs: 99.8 % / Redundancy: 6.031 % / Biso Wilson estimate: 25.98 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rrim(I) all: 0.103 / Χ2: 0.966 / Net I/σ(I): 13.68
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.156.1340.4993.7524300.8850.545100
2.15-2.216.1770.4364.223220.8940.476100
2.21-2.286.1650.3655.0422760.9340.39899.9
2.28-2.356.1410.345.4222400.9520.37199.9
2.35-2.426.1640.2646.7521330.9650.28899.9
2.42-2.516.1190.2188.0220600.9720.238100
2.51-2.66.1310.1978.7720260.980.215100
2.6-2.716.1140.15510.8519370.9850.16999.9
2.71-2.836.0980.13412.3618450.9880.14699.9
2.83-2.976.0830.11214.0517970.9920.122100
2.97-3.135.9940.09216.8217000.9940.10199.9
3.13-3.325.9990.0782016250.9940.08599.9
3.32-3.555.9050.06522.9915340.9960.07199.9
3.55-3.835.9030.05924.8414010.9970.06599.6
3.83-4.25.8580.05426.8413080.9970.0699.8
4.2-4.75.8470.04928.7512070.9970.05499.8
4.7-5.425.8250.04728.9310770.9950.05299.9
5.42-6.645.7630.04427.99090.9970.04999.9
6.64-9.395.5710.03729.147280.9980.04199.3
9.39-504.9710.03329.214200.9960.03895.9

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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: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2563 1649 5 %
Rwork0.1982 --
obs0.2011 32967 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.54 Å2 / Biso mean: 39.9097 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 186 340 3777
Biso mean--50.5 30.44 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083569
X-RAY DIFFRACTIONf_angle_d0.8384891
X-RAY DIFFRACTIONf_chiral_restr0.05585
X-RAY DIFFRACTIONf_plane_restr0.005601
X-RAY DIFFRACTIONf_dihedral_angle_d14.0572163
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16180.32231360.2352570100
2.1618-2.23160.29041350.22452568100
2.2316-2.31130.24441350.21582576100
2.3113-2.40390.28091360.21382565100
2.4039-2.51330.26031360.22583100
2.5133-2.64580.27781360.2152582100
2.6458-2.81150.28691370.21142605100
2.8115-3.02860.30181360.21852580100
3.0286-3.33330.2571380.20252629100
3.3333-3.81540.24711370.18642617100
3.8154-4.80620.21561400.15262667100
4.8062-500.23021470.2064277699
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)
11.6161-0.25171.15671.4516-0.64713.593-0.0496-0.3881-0.26930.267-0.0623-0.12960.27380.33770.07880.31230.0203-0.010.37810.12940.30229.4139-12.4767-12.1786
27.7089-1.21532.1551.5638-1.22131.34520.2026-0.772-0.94680.19170.13610.19830.0321-0.1518-0.39440.4260.0612-0.02160.50050.1740.395210.1951-16.9491-6.3778
32.6597-0.83651.79362.995-2.32982.3594-0.1926-0.3942-0.08060.35820.13720.14180.0382-0.18930.13440.33810.08490.02980.35650.08170.27944.111-8.3155-11.7815
42.95270.4441-0.50633.024-0.31622.3931-0.11130.0362-0.2506-0.07520.0195-0.07660.06410.16780.08710.2098-0.00990.01620.1771-0.00060.244319.0672-2.5551-39.2921
52.97870.2922-0.22033.2585-0.01042.2029-0.16910.1791-0.2191-0.29990.1136-0.40090.14250.13030.03680.2952-0.00160.05070.1571-0.01570.283518.9167-7.9746-44.2087
61.4312-0.1092-0.08832.7915-0.31653.4081-0.0472-0.66580.40770.3752-0.24640.2451-0.2387-0.36090.13110.3116-0.02080.04390.4768-0.12710.291538.944819.5592-15.6375
72.59080.7361-1.80815.29880.42065.48950.5313-0.57661.36070.3179-0.0984-0.1315-0.7427-0.4909-0.39510.43990.015-0.0310.4671-0.13740.398937.396624.3443-10.3463
82.50430.064-0.28273.64342.35192.3448-0.0464-0.5515-0.07860.3273-0.1398-0.17260.22370.06760.09980.26780.0275-0.01950.38060.0580.27344.413612.6716-18.0075
94.2230.0071.10262.056-0.50243.3433-0.07710.24510.2835-0.16510.00590.0976-0.09550.02330.08340.2148-0.0180.00250.17540.01410.260229.3018.9416-43.6159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 240 through 282 )A240 - 282
2X-RAY DIFFRACTION2chain 'A' and (resid 283 through 304 )A283 - 304
3X-RAY DIFFRACTION3chain 'A' and (resid 305 through 339 )A305 - 339
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 406 )A340 - 406
5X-RAY DIFFRACTION5chain 'A' and (resid 407 through 446 )A407 - 446
6X-RAY DIFFRACTION6chain 'B' and (resid 240 through 282 )B240 - 282
7X-RAY DIFFRACTION7chain 'B' and (resid 283 through 304 )B283 - 304
8X-RAY DIFFRACTION8chain 'B' and (resid 305 through 349 )B305 - 349
9X-RAY DIFFRACTION9chain 'B' and (resid 350 through 446 )B350 - 446

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