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- PDB-5ir1: Cetuximab Fab in complex with 3-bromophenylalanine meditope variant -

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Basic information

Entry
Database: PDB / ID: 5ir1
TitleCetuximab Fab in complex with 3-bromophenylalanine meditope variant
Components
  • (Cetuximab Fab ...) x 2
  • Meditope variant
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: 2.482 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
DepositionMar 11, 2016Deposition 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _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_label_seq_id
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

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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: Meditope variant
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,54611
Polymers96,9456
Non-polymers6015
Water9,116506
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8846
Polymers48,4733
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-32 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: Meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6635
Polymers48,4733
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-37 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.040, 82.510, 211.540
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: 23725.504 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, 3 molecules EF

#3: Protein/peptide Meditope variant


Mass: 1459.470 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.: 1
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, 510 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.: 506 / Source method: isolated from a natural source / Formula: H2O

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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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citric acid, 0.1 M sodium hydrogen phosphate, 0.4 M potassium hydrogen phosphate, 1.6 M sodium dihydrogen phosphate

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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: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→34.225 Å / Num. obs: 40296 / % possible obs: 99.4 % / Redundancy: 5.8 % / Net I/σ(I): 30.1
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 8.9

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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: 2.482→34.225 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.2149 2014 5 %
Rwork0.1632 --
obs0.1657 40287 99.5 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.482→34.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6760 0 34 506 7300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086989
X-RAY DIFFRACTIONf_angle_d1.189539
X-RAY DIFFRACTIONf_dihedral_angle_d12.2214153
X-RAY DIFFRACTIONf_chiral_restr0.0781078
X-RAY DIFFRACTIONf_plane_restr0.0051221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4825-2.54450.31311320.1992510X-RAY DIFFRACTION94
2.5445-2.61330.31311430.19052709X-RAY DIFFRACTION100
2.6133-2.69020.24481410.18022695X-RAY DIFFRACTION100
2.6902-2.7770.27431430.18212718X-RAY DIFFRACTION100
2.777-2.87620.24251430.17762701X-RAY DIFFRACTION100
2.8762-2.99130.21421430.17632726X-RAY DIFFRACTION100
2.9913-3.12730.25451430.18222707X-RAY DIFFRACTION100
3.1273-3.29210.25911440.18412739X-RAY DIFFRACTION100
3.2921-3.49810.20391430.15882729X-RAY DIFFRACTION100
3.4981-3.76790.20071460.15152759X-RAY DIFFRACTION100
3.7679-4.14650.181440.14252751X-RAY DIFFRACTION100
4.1465-4.74520.16221470.11712778X-RAY DIFFRACTION100
4.7452-5.97320.171470.14342812X-RAY DIFFRACTION100
5.9732-34.22780.21041550.19922939X-RAY DIFFRACTION100
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)
16.7986-0.59860.67912.289-3.71457.90540.20140.5526-0.3089-0.12240.22660.7931-0.3403-0.8283-0.40980.28240.07440.0020.4611-0.02390.282116.0702-32.0399-15.0318
22.90480.70681.11372.6545-1.05563.27560.0204-0.1350.2464-0.228-0.0157-0.0703-0.79870.2357-0.00460.5014-0.00210.07710.2112-0.02630.199329.9637-24.6407-14.2346
32.83280.7336-1.02283.628-0.63252.73010.0498-0.20360.3102-0.14510.12780.2197-0.6488-0.1457-0.11990.34720.05140.00830.2592-0.04180.148625.9895-29.4157-16.901
40.62381.3839-2.19512.9362-4.71637.45140.0856-0.17020.16680.74380.31440.3098-0.34620.1458-0.39950.450.07440.08960.2569-0.00330.233224.9677-18.0622-35.1004
54.1576-0.8477-0.15225.80813.22956.3260.38210.3529-0.3932-0.0428-0.2456-0.6250.550.3874-0.16550.180.05610.01590.2689-0.0110.210534.32-36.2834-57.7552
62.13041.19841.68356.15755.96656.725-0.1623-0.07050.16960.07050.08990.3668-0.0555-0.22640.06130.1155-0.02640.06080.16370.02970.23424.6658-27.2084-50.5099
73.22081.46914.07922.22812.92495.8884-0.00130.13780.20380.01070.04480.2551-0.1605-0.2203-0.10770.1252-0.0456-0.03650.2794-0.01150.314119.8363-33.5553-55.2011
88.07663.42955.53359.14244.90024.64060.1237-0.8961-0.14310.9514-0.29340.39060.3283-0.40320.2080.26570.01330.05280.23920.03440.220530.2681-22.5539-36.9931
92.6549-0.12180.38155.45141.61294.12790.09780.53560.0336-0.5272-0.16620.3903-0.03880.13020.07770.12570.0134-0.06240.2502-0.00490.209525.586-30.1047-59.8015
102.05850.70650.89671.56520.98675.42460.0685-0.0826-0.1851-0.02980.0066-0.09690.290.1259-0.06640.20260.01730.00480.17050.02350.181733.2512-47.0119-16.9237
114.85443.4114-1.14363.51270.0913.3748-0.10310.17980.2707-0.46920.04290.44130.1614-0.0028-0.06490.08370.0296-0.01410.1705-0.04510.19535.8195-37.5663-49.815
121.48641.7023-0.66944.2364-1.13591.4746-0.0532-0.0251-0.0749-0.0203-0.05850.0186-0.0153-0.0630.09370.12610.00810.01680.1986-0.04650.167236.455-35.2414-43.6079
136.79674.0657-2.55167.4668-3.98515.7498-0.0927-0.3056-0.1409-0.0657-0.1994-0.47460.25160.20980.23870.0840.04310.01670.1950.03060.233344.7947-39.0575-46.9233
143.0573.98833.7096.62695.00587.41350.20140.4411-0.1514-0.46640.2528-0.83460.46060.6418-0.44780.45990.1510.08680.28970.00340.336611.3484-16.7228-19.5423
153.43040.4374-0.57163.59791.39693.49240.00410.0141-0.2479-0.09310.0277-0.03140.2969-0.0543-0.05110.29910.03730.00960.16430.06240.20263.5802-14.813-14.0064
160.47310.2160.04571.75053.66036.1083-0.0056-0.1284-0.1790.11070.2454-0.17920.34930.4425-0.26270.3870.0785-0.02450.19150.03490.21887.6642-12.1766-21.531
171.73010.7472-1.24842.7156-1.67943.4765-0.12520.1383-0.1198-0.1810.0933-0.11610.1425-0.04020.03680.0969-0.02220.00050.1798-0.02630.18525.2444-7.1834-52.4013
188.76363.0619-5.41887.4431-5.23267.5662-0.03480.3850.2460.14780.13950.1505-0.5077-0.242-0.14620.27010.0507-0.01250.2621-0.05430.1776-3.213710.3399-22.5875
190.3524-0.06240.09520.0648-0.19413.92340.0298-0.13230.07560.02520.03450.0173-0.3198-0.0449-0.06350.23450.0320.01520.16810.01230.1744-1.03746.89-15.7453
203.63440.4205-0.44723.863-3.75823.6444-0.35030.4006-0.3673-1.57570.24740.23180.0374-0.1636-0.04420.1983-0.02380.00120.24280.02130.2605-5.217-6.073-50.9163
211.33650.84741.08364.17650.83752.28110.05920.0829-0.05310.17220.0325-0.0497-0.0759-0.039-0.05940.1147-0.0060.01090.13110.03220.1619-4.3347-2.5147-41.3235
224.55782.49821.68736.23.40925.5689-0.0037-0.18230.2052-0.2971-0.31630.5145-0.1467-0.61360.32280.09540.02810.0090.22910.02580.2617-12.84931.1295-45.1729
236.55051.1184-2.44118.64650.42698.728-0.4775-0.4821-1.2652-1.05980.23670.14090.1813-0.22160.25270.76380.09510.0360.39620.13960.427123.9906-35.6938-30.5683
240.4156-0.4153-1.46297.76293.9077.06490.2247-0.24480.3583-1.7212-0.368-0.0256-0.69190.09810.18860.7040.03860.12680.38960.0290.29057.6808-3.4074-28.8591
251.09150.2125-0.07941.0802-0.42622.08640.2014-0.02420.171-0.25920.02510.2617-0.28180.0599-0.23410.4550.0910.06050.2201-0.01960.224622.3987-24.6686-16.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1:8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39:75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76:101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102:113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114:128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129:150 )
7X-RAY DIFFRACTION7chain 'A' and (resid 151:163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164:174 )
9X-RAY DIFFRACTION9chain 'A' and (resid 175:213 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1:117 )
11X-RAY DIFFRACTION11chain 'B' and (resid 118:151 )
12X-RAY DIFFRACTION12chain 'B' and (resid 152:195 )
13X-RAY DIFFRACTION13chain 'B' and (resid 196:220 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1:18 )
15X-RAY DIFFRACTION15chain 'C' and (resid 19:90 )
16X-RAY DIFFRACTION16chain 'C' and (resid 91:113 )
17X-RAY DIFFRACTION17chain 'C' and (resid 114:213 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1:17 )
19X-RAY DIFFRACTION19chain 'D' and (resid 18:130 )
20X-RAY DIFFRACTION20chain 'D' and (resid 131:151 )
21X-RAY DIFFRACTION21chain 'D' and (resid 152:194 )
22X-RAY DIFFRACTION22chain 'D' and (resid 195:220 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1:12 )
24X-RAY DIFFRACTION24chain 'F' and (resid 1:12 )
25X-RAY DIFFRACTION25chain 'A' and (resid 9:38 )

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