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- PDB-6ugv: Crystal structure of the Fab fragment of anti-TNFa antibody infli... -

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Basic information

Entry
Database: PDB / ID: 6ugv
TitleCrystal structure of the Fab fragment of anti-TNFa antibody infliximab (Remicade) in a I-centered orthorhombic crystal form, Lot C
Components
  • Infliximab Fab Heavy Chain
  • Infliximab Fab Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / infliximab / biosimilar / TNFa
Function / homology
Function and homology information


immunoglobulin complex / 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 C1-set domain ...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
MESO-ERYTHRITOL / Ig-like domain-containing protein / IGK@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLerch, T.F. / Sharpe, P. / Mayclin, S.J. / Edwards, T.E. / Polleck, S. / Rouse, J.C. / Conlan, H.D.
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: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Infliximab Fab Heavy Chain
L: Infliximab Fab Light Chain
A: Infliximab Fab Heavy Chain
B: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0659
Polymers95,6344
Non-polymers4305
Water11,079615
1
H: Infliximab Fab Heavy Chain
L: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0014
Polymers47,8172
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-23 kcal/mol
Surface area18900 Å2
MethodPISA
2
A: Infliximab Fab Heavy Chain
B: Infliximab Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0635
Polymers47,8172
Non-polymers2463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-21 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.660, 93.300, 315.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11H-448-

HOH

21H-457-

HOH

31A-542-

HOH

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Components

#1: Antibody Infliximab Fab Heavy Chain


Mass: 24356.178 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: A8K008
#2: Antibody Infliximab Fab Light Chain


Mass: 23460.873 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: Q6P5S8
#3: Chemical ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10 mg/mL PF06438179 Fab lot A against 2.16 M sodium malonate, 4% pentaerythritol ethoxylate, crystal tracking ID 267670e4, unique puck ID sar8-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 19, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 52789 / % possible obs: 99.9 % / Redundancy: 6.19 % / Biso Wilson estimate: 31.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rrim(I) all: 0.137 / Χ2: 0.946 / Net I/σ(I): 12.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.466.2820.792.6838600.7910.86199.9
2.46-2.536.2760.6693.1337400.8510.7399.9
2.53-2.66.2920.5793.6236840.8680.632100
2.6-2.686.2810.4474.5735060.9120.48899.9
2.68-2.776.2880.3635.5334790.9450.395100
2.77-2.876.2770.3026.4133360.9590.33100
2.87-2.986.2650.247.9632230.9720.26299.9
2.98-3.16.260.18410.0331540.9820.20199.9
3.1-3.246.2460.14312.2729680.9890.15599.9
3.24-3.396.2160.11514.6128410.9930.12699.9
3.39-3.586.1780.09916.6527230.9940.10999.8
3.58-3.796.170.08718.5825950.9950.095100
3.79-4.066.1490.07321.2824380.9960.0899.9
4.06-4.386.1010.06124.8822570.9970.06799.8
4.38-4.86.0560.05526.9820960.9970.0699.9
4.8-5.376.0750.05526.4719190.9970.06199.9
5.37-6.26.0390.06124.1117020.9970.06699.9
6.2-7.595.9570.05824.614500.9970.064100
7.59-10.735.7610.04431.0311500.9980.048100
10.73-505.10.04429.426680.9980.04997.8

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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 4G3Y

4g3y


Resolution: 2.4→50 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.41
RfactorNum. reflection% reflection
Rfree0.2099 2620 4.96 %
Rwork0.1527 --
obs0.1555 52775 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.66 Å2 / Biso mean: 34.8659 Å2 / Biso min: 13.4 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 28 615 7213
Biso mean--87.42 41.34 -
Num. residues----868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066786
X-RAY DIFFRACTIONf_angle_d0.8489242
X-RAY DIFFRACTIONf_chiral_restr0.0521037
X-RAY DIFFRACTIONf_plane_restr0.0041185
X-RAY DIFFRACTIONf_dihedral_angle_d13.4064029
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4001-2.44370.25381340.212600
2.4437-2.49070.28781350.22382585
2.4907-2.54160.3081420.21632624
2.5416-2.59680.24661170.20482627
2.5968-2.65720.2881430.19072604
2.6572-2.72370.25851310.18652597
2.7237-2.79730.22661320.18232637
2.7973-2.87960.23261230.17572622
2.8796-2.97260.23861470.18272598
2.9726-3.07880.23091610.17552600
3.0788-3.2020.21931710.16482596
3.202-3.34770.18241560.1472640
3.3477-3.52410.22851370.13942618
3.5241-3.74490.20661280.13462645
3.7449-4.03390.20341110.12552672
4.0339-4.43950.15381170.1062685
4.4395-5.08120.14421350.10372679
5.0812-6.39920.15711220.14722724
6.3992-500.20791780.16832802
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)
12.97331.1621.5542.63841.1563.1706-0.01020.13770.0343-0.08050.0029-0.1002-0.12970.1240.00320.18-0.0273-0.0040.19560.01540.1456-10.86856.236711.0095
21.2921-1.1180.94681.958-0.53831.6818-0.2409-0.0310.2240.29730.0835-0.50780.00030.2750.10910.2242-0.0089-0.04920.24380.01340.34965.6897-1.232235.7014
31.8255-0.13760.31946.9667-1.6411.6717-0.17870.11720.2892-0.13840.0532-0.5122-0.1470.17160.12460.2296-0.0511-0.03510.20840.02180.25896.0124-6.547633.4543
43.1211-3.39973.91644.5208-5.98258.3404-0.0234-0.3726-0.33930.30130.08340.13310.0667-0.3587-0.06810.2378-0.0539-0.0050.320.05870.2353-27.6965-4.732830.3306
52.8227-1.4722-0.01434.8951-1.19294.00670.0457-0.037-0.4376-0.10820.01180.18420.3019-0.1604-0.06380.1805-0.0666-0.04180.2386-0.00890.1919-26.7211-7.218420.0717
60.6525-0.990.99631.2215-1.13642.4631-0.1266-0.0643-0.07810.04420.20860.01390.0041-0.1489-0.15770.1923-0.0231-0.00650.14810.00020.2033-12.8126-6.132.3783
74.87391.75771.30352.90960.73241.9007-0.1432-0.18230.15340.36980.1773-0.1744-0.25940.0618-0.00170.29630.0521-0.06810.2093-0.0140.2108-4.2965-5.519647.1288
88.23613.13170.97263.46860.12871.8827-0.0291-0.99870.06420.5499-0.1173-0.4345-0.18040.22050.13420.42940.0808-0.14380.3678-0.05090.25284.1586-5.378554.1215
91.84140.2555-0.13522.8137-1.32393.8099-0.0623-0.0510.23720.24660.0213-0.0681-0.02630.04340.02530.19-0.0309-0.01230.17-0.01750.2055-15.655512.862166.4616
103.94151.2082-1.94913.5848-1.21332.28180.46650.80180.6584-0.139-0.323-0.02320.06120.1277-0.20860.23150.09330.0340.2592-0.00940.3523-33.435831.647535.1737
117.9696-0.8021.64722.2044-0.88762.39740.0342-0.28520.54680.2261-0.1096-0.2207-0.28220.11860.05270.2112-0.04720.00230.191-0.0210.2286-28.195228.754245.1591
123.7518-1.44161.52862.4529-0.46254.14560.06860.0287-0.09890.03190.01180.42160.2503-0.2864-0.0750.2671-0.09940.00690.19190.02120.2369-29.1599-4.182556.6212
131.0239-0.88710.99531.0181-0.77072.41110.2051-0.0303-0.0028-0.0566-0.07160.18590.1592-0.0451-0.17870.1592-0.03430.02310.17980.00470.2171-28.429810.134646.4941
144.01512.4606-0.53663.6272-0.98251.30430.15960.43890.0004-0.0807-0.0202-0.0906-0.04490.1153-0.08590.20810.0593-0.00150.28870.01570.1828-27.789218.059731.8898
154.732.73260.56445.9936-0.09472.7104-0.2190.73580.5164-0.63190.1417-0.0219-0.3250.35290.0540.29540.02840.01980.38250.11490.2493-26.98626.83924.5625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 113 )H1 - 113
2X-RAY DIFFRACTION2chain 'H' and (resid 114 through 141 )H114 - 141
3X-RAY DIFFRACTION3chain 'H' and (resid 142 through 220 )H142 - 220
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 18 )L1 - 18
5X-RAY DIFFRACTION5chain 'L' and (resid 19 through 75 )L19 - 75
6X-RAY DIFFRACTION6chain 'L' and (resid 76 through 128 )L76 - 128
7X-RAY DIFFRACTION7chain 'L' and (resid 129 through 174 )L129 - 174
8X-RAY DIFFRACTION8chain 'L' and (resid 175 through 213 )L175 - 213
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 126 )A1 - 126
10X-RAY DIFFRACTION10chain 'A' and (resid 127 through 141 )A127 - 141
11X-RAY DIFFRACTION11chain 'A' and (resid 142 through 220 )A142 - 220
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 75 )B1 - 75
13X-RAY DIFFRACTION13chain 'B' and (resid 76 through 128 )B76 - 128
14X-RAY DIFFRACTION14chain 'B' and (resid 129 through 174 )B129 - 174
15X-RAY DIFFRACTION15chain 'B' and (resid 175 through 213 )B175 - 213

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