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- PDB-5f88: Cetuximab Fab in complex with L5Y meditope variant -

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Basic information

Entry
Database: PDB / ID: 5f88
TitleCetuximab Fab in complex with L5Y meditope variant
Components
  • (Cetuximab Fab ...) x 2
  • L5Y meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.481 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
E: L5Y meditope
F: L5Y meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,72012
Polymers96,8986
Non-polymers8226
Water9,224512
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: L5Y meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8606
Polymers48,4493
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-36 kcal/mol
Surface area18700 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: L5Y meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8606
Polymers48,4493
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-36 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.240, 83.140, 211.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Cetuximab Fab light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)
#2: Antibody Cetuximab Fab heavy chain


Mass: 23638.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others)

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Protein/peptide / Sugars , 2 types, 4 molecules EF

#3: Protein/peptide L5Y meditope


Mass: 1522.772 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 516 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate, 0.1 M Na2HPO4, 0.5 M K2HPO4, 1.6 M NaH2PO4
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→33.15 Å / Num. obs: 39080 / % possible obs: 95.1 % / Redundancy: 5.2 % / Net I/σ(I): 25.2
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 9.2 / % possible all: 72.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.481→32.706 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 1955 5 %
Rwork0.1626 --
obs0.1653 39079 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.481→32.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 0 48 512 7298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036995
X-RAY DIFFRACTIONf_angle_d0.6649545
X-RAY DIFFRACTIONf_dihedral_angle_d10.4184175
X-RAY DIFFRACTIONf_chiral_restr0.0471076
X-RAY DIFFRACTIONf_plane_restr0.0041221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4812-2.54320.24521040.18551979X-RAY DIFFRACTION72
2.5432-2.61190.2541330.19612514X-RAY DIFFRACTION92
2.6119-2.68880.27651400.19812678X-RAY DIFFRACTION96
2.6888-2.77550.27361390.19752626X-RAY DIFFRACTION96
2.7755-2.87470.24911390.17992650X-RAY DIFFRACTION97
2.8747-2.98970.24541400.18042660X-RAY DIFFRACTION97
2.9897-3.12560.21941400.1882662X-RAY DIFFRACTION97
3.1256-3.29030.25361420.18842702X-RAY DIFFRACTION97
3.2903-3.49620.21651430.16552700X-RAY DIFFRACTION97
3.4962-3.76580.19971430.15272725X-RAY DIFFRACTION97
3.7658-4.14410.1941430.13462726X-RAY DIFFRACTION98
4.1441-4.74220.16951450.11642741X-RAY DIFFRACTION98
4.7422-5.96870.16371480.13442816X-RAY DIFFRACTION98
5.9687-32.70840.23261560.18372945X-RAY DIFFRACTION98
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)
12.81922.0676-1.17224.6267-3.85454.20450.20230.05450.0050.3632-0.09850.2039-0.4996-0.1493-0.15680.28690.0630.04570.1906-0.05150.285619.43-23.6507-20.5498
21.23830.0140.30452.2698-0.47752.69850.1633-0.03110.10350.35930.03510.1953-0.4373-0.1627-0.15880.2957-0.040.07710.2256-0.04760.187626.9736-26.1411-13.4757
30.39920.28110.06830.693-0.87011.62080.0602-0.0488-0.0370.1222-0.00970.1379-0.26230.1738-0.05280.16170.03520.03160.1798-0.02280.164628.247-29.1335-32.6141
41.1503-0.16530.14823.69493.38924.1019-0.1271-0.001-0.02160.07220.07560.2339-0.0522-0.18140.04080.1154-0.01240.05310.1350.00990.21924.8062-27.2184-50.6959
52.1840.0051.23391.11550.98173.5218-0.06390.07370.5152-0.13290.04620.27630.096-0.14180.08080.1454-0.04350.02510.19590.00790.242420.0767-33.5586-55.5383
61.8245-0.14120.71862.35891.19361.94770.01310.13630.0243-0.1393-0.04110.085-0.03650.09630.02380.1364-0.02040.0380.17350.00770.153726.8631-28.1935-54.8462
71.65770.16370.16741.6449-0.34683.23660.0054-0.031-0.12060.05380.0042-0.09610.19040.40390.05190.18350.0369-0.01360.2698-0.01320.192638.5796-48.0677-20.0128
81.63930.278-0.16192.0033-0.26362.4757-0.0009-0.33310.0595-0.01560.03720.07850.5482-0.1291-0.03090.2201-0.0237-0.01970.1667-0.03190.152928.8649-48.6286-13.9139
94.39840.79361.94151.13870.66674.13580.1898-0.4694-0.2443-0.0836-0.08920.09250.6973-0.1082-0.07320.351-0.0244-0.04040.1882-0.03050.21132.5939-53.1509-20.3454
100.85560.55920.22620.5473-0.50932.26060.2686-0.1472-0.00590.2456-0.0623-0.08380.16740.0814-0.13780.2052-0.0017-0.00410.2569-0.02230.162334.0965-40.0139-11.8414
111.11610.4945-0.22990.1907-0.20042.74440.05530.01670.0620.0117-0.00110.00930.1802-0.148-0.01450.15380.04640.02190.1013-0.01480.198234.8271-41.3937-37.2912
121.04141.219-0.38012.8554-1.35751.69350.0042-0.18970.11620.12590.0309-0.0031-0.04120.1018-0.03130.09120.0304-0.02270.1566-0.04320.227137.6557-38.1784-44.0768
130.80570.05130.33791.5621-0.66291.1865-0.1186-0.03810.102-0.0843-0.04320.02180.01680.03280.16840.1545-0.00580.01970.1343-0.04930.192735.1679-33.5629-44.972
142.17960.9166-0.27193.5771-1.30562.3684-0.0905-0.186-0.1493-0.1784-0.1603-0.59090.01180.19920.20650.11750.03360.04110.21350.01880.216845.2127-37.3546-45.0625
153.30851.3277-1.16678.25-4.77396.8295-0.2205-0.4045-0.2335-0.44470.0152-0.34280.2260.35870.19790.17080.02180.02430.15970.05460.320245.0415-39.8393-49.8843
163.4661.9141.55815.26732.87495.9130.42160.1291-0.39490.23180.0733-0.26090.5190.3188-0.4480.24680.0864-0.02240.1878-0.00770.237412.0619-16.6356-17.806
171.3182-0.5829-0.99432.04050.40532.50990.01590.0413-0.17520.1440.16750.17040.4937-0.065-0.16210.2650.0041-0.03610.20710.04510.15923.0766-14.029-11.9109
181.0229-0.5959-0.44251.37040.56752.05570.0129-0.1111-0.12570.20490.1384-0.10620.29880.1049-0.0940.25990.0234-0.04490.20830.00320.13855.4211-10.763-15.6552
190.2340.47970.6821.72772.75144.42850.1437-0.3349-0.08720.4174-0.0126-0.15320.5865-0.0649-0.18980.31620.023-0.03720.19110.02070.18946.6163-20.2837-34.3121
201.38150.4977-0.81651.00510.34310.98740.27940.4690.3074-0.2215-0.36550.2371-0.0596-0.2648-0.06360.17120.0002-0.02120.18320.06630.227-2.49650.7413-55.4259
210.4674-0.001-0.54623.9703-2.65452.3661-0.23790.0592-0.06970.02290.1528-0.40510.01660.23310.11030.1075-0.03-0.02980.1796-0.00470.23986.9839-9.9033-49.0589
221.06120.595-1.16411.5878-1.2491.9663-0.0703-0.0656-0.14350.060.055-0.09660.09690.1506-0.01260.1282-0.0197-0.00920.1913-0.02840.186.928-9.1191-45.0413
231.25360.0354-0.14413.6855-1.61983.113-0.04040.20350.0613-0.34750.002-0.03790.16730.08240.02840.118-0.01980.02120.16620.01960.15866.1908-6.1958-58.1242
240.82870.5971-0.12131.3458-0.07382.67530.0035-0.0920.09460.09170.05660.0268-0.298-0.1732-0.06970.21290.08080.00980.21280.00510.1693-1.22427.1637-13.9138
251.1866-0.2619-0.37331.4712-1.58332.0599-0.07580.101-0.1673-0.19370.2581-0.3063-0.3365-0.0245-0.17060.06230.0284-0.00910.1644-0.05520.2183-2.96016.1524-45.5679
262.0620.92930.80852.68291.2231.7297-0.0493-0.1314-0.0292-0.0182-0.03790.208-0.0599-0.16590.09660.11340.02640.01140.12140.03050.1519-7.2007-0.5943-43.2776
272.64171.3298-1.892.68070.91813.70460.3635-0.0275-0.0286-0.7665-0.27630.7594-0.2702-0.0096-0.22990.27210.0346-0.07830.16060.00210.311523.6564-35.4803-30.6927
282.3095-1.0104-0.50574.79421.20932.24870.319-0.0367-0.0709-0.7332-0.1102-0.68570.25870.3629-0.24180.22880.10510.04580.30730.0450.25298.0291-3.6048-28.4807
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 163 )
6X-RAY DIFFRACTION6chain 'A' and (resid 164 through 213 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 72 )
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 90 )
10X-RAY DIFFRACTION10chain 'B' and (resid 91 through 105 )
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 140 )
12X-RAY DIFFRACTION12chain 'B' and (resid 141 through 163 )
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 194 )
14X-RAY DIFFRACTION14chain 'B' and (resid 195 through 209 )
15X-RAY DIFFRACTION15chain 'B' and (resid 210 through 220 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 25 )
17X-RAY DIFFRACTION17chain 'C' and (resid 26 through 75 )
18X-RAY DIFFRACTION18chain 'C' and (resid 76 through 101 )
19X-RAY DIFFRACTION19chain 'C' and (resid 102 through 113 )
20X-RAY DIFFRACTION20chain 'C' and (resid 114 through 128 )
21X-RAY DIFFRACTION21chain 'C' and (resid 129 through 150 )
22X-RAY DIFFRACTION22chain 'C' and (resid 151 through 174 )
23X-RAY DIFFRACTION23chain 'C' and (resid 175 through 213 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 117 )
25X-RAY DIFFRACTION25chain 'D' and (resid 118 through 140 )
26X-RAY DIFFRACTION26chain 'D' and (resid 141 through 220 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 12 )
28X-RAY DIFFRACTION28chain 'F' and (resid 1 through 12 )

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