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- PDB-5t1l: Cetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide -

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Basic information

Entry
Database: PDB / ID: 5t1l
TitleCetuximab Fab in complex with CQA(Ph)2DLSTRRLKC peptide
Components
  • (CETUXIMAB FAB HEAVY ...) x 2
  • CETUXIMAB FAB LIGHT CHAIN
  • CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
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: 2.48 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
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
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
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Jul 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 2.2Oct 4, 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 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
F: CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,02413
Polymers97,1076
Non-polymers9177
Water9,872548
1
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
E: CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9566
Polymers48,5453
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-36 kcal/mol
Surface area18940 Å2
MethodPISA
2
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
F: CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0687
Polymers48,5623
Non-polymers5064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-45 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.050, 82.970, 211.960
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 , 3 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: 23708.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: unidentified (others)
#3: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23725.504 Da / Num. of mol.: 1
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

#4: Protein/peptide CYCLIC MEDITOPE CQA(Ph)2DLSTRRLKC


Mass: 1548.852 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: 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 / N-Acetylglucosamine


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, 553 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.4 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, pH 5.5
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: Aug 19, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→34.4 Å / Num. obs: 40655 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 24.9
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5 / % possible all: 92.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.48→34.36 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.16
RfactorNum. reflection% reflection
Rfree0.204 2031 5 %
Rwork0.158 --
obs0.16 40642 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.48→34.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 53 548 7357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087025
X-RAY DIFFRACTIONf_angle_d1.1789566
X-RAY DIFFRACTIONf_dihedral_angle_d13.9382521
X-RAY DIFFRACTIONf_chiral_restr0.0731078
X-RAY DIFFRACTIONf_plane_restr0.0051224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.53780.24071210.19042302X-RAY DIFFRACTION89
2.5378-2.60130.29211300.18762536X-RAY DIFFRACTION100
2.6013-2.67160.25151380.18082571X-RAY DIFFRACTION100
2.6716-2.75010.25791360.17442545X-RAY DIFFRACTION100
2.7501-2.83890.24251340.17962551X-RAY DIFFRACTION100
2.8389-2.94030.2391340.18542545X-RAY DIFFRACTION100
2.9403-3.05790.251350.18342598X-RAY DIFFRACTION100
3.0579-3.1970.24721350.17442572X-RAY DIFFRACTION100
3.197-3.36540.2021380.16132568X-RAY DIFFRACTION100
3.3654-3.57610.21961330.15092575X-RAY DIFFRACTION100
3.5761-3.85180.17491370.14332587X-RAY DIFFRACTION100
3.8518-4.23880.16381370.13592609X-RAY DIFFRACTION100
4.2388-4.85070.17551380.11442618X-RAY DIFFRACTION100
4.8507-6.10580.16091400.13842654X-RAY DIFFRACTION100
6.1058-34.36220.17731450.1852780X-RAY DIFFRACTION99
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)
11.6058-0.82810.32511.4627-0.88832.25810.18880.097-0.116-0.0483-0.00810.11910.3736-0.0615-0.13050.2273-0.0499-0.03810.2017-0.02320.193419.199123.687919.3301
20.72620.0744-0.47730.8288-0.20381.30820.03130.0539-0.1420.04760.05330.06310.20190.0442-0.04670.15180.0208-0.03080.1234-0.02930.097427.116627.690314.787
30.85350.0127-0.38420.4471-0.51210.73480.0321-0.0925-0.0245-0.06130.1696-0.0664-0.03650.2038-0.08710.1283-0.0048-0.0220.0467-0.00710.126530.086428.374347.8974
40.7387-0.2833-0.1531.28851.37522.3775-0.05150.036-0.07410.0966-0.01030.246-0.31920.00810.065-0.10070.0198-0.00550.1026-0.00450.238424.642727.278950.7569
50.999-0.2847-0.61980.510.95711.7827-0.0865-0.00810.00740.07650.029-0.01110.07740.12740.03810.11540.03430.03640.17770.01640.223819.849633.624755.5375
61.11370.2788-0.73221.3716-0.47460.54290.0932-0.14270.01880.1401-0.01250.0173-0.06810.0476-0.05910.06520.0035-0.01040.0978-0.04110.13226.662628.393154.8988
71.3332-0.5513-1.28961.02881.0162.7547-0.0907-0.46430.18650.01730.3329-0.2193-0.22620.4798-0.02150.23990.00120.03170.182-0.03330.25635.541749.423625.7657
80.12580.0310.47720.1832-0.18691.580.0130.08370.036-0.0492-0.0049-0.0285-0.23030.003-0.01450.14730.00470.01720.112-0.01190.13633.004747.058418.8263
91.3777-1.06570.29273.402-0.44091.4294-0.19680.0032-0.08480.14520.1295-0.1186-0.0155-0.06220.00030.0509-0.00830.01590.1714-0.00720.132537.058433.703950.9032
100.5766-0.1566-0.15631.2303-0.07730.3861-0.0280.0979-0.076-0.0105-0.0460.0417-0.0543-0.00270.05470.09260.0061-0.00140.1022-0.03480.148236.1835.530943.5204
112.2439-1.7010.72913.4896-1.55092.3897-0.00870.19360.13210.2298-0.1449-0.425-0.20290.2622-0.0170.0809-0.041-0.00620.13720.01430.182844.960838.626947.3821
12222.0001222-1.4332.1953-0.5678-1.70821.30982.8257-0.1534-1.44740.18091.0317-0.0169-0.27781.1683-0.51430.844125.30144.14737.35
131.4697-1.1328-0.7573.24021.58173.01820.243-0.05440.1580.2276-0.0958-0.2701-0.17630.1274-0.12370.1986-0.07230.00910.18350.00690.211411.916916.818817.6508
140.4740.12350.46980.90030.15691.5597-0.00550.0530.10390.0190.1330.0745-0.1207-0.0477-0.12710.1582-0.02570.00190.1280.02210.11953.05514.036611.8166
150.84380.4041-0.24410.90470.6191.33150.0340.05470.06510.03960.107-0.12610.02730.0359-0.08760.1895-0.0024-0.01910.13330.01290.10015.398310.868915.5131
160.40950.14150.21230.49760.58090.7005-0.0202-0.0133-0.0018-0.04380.06940.0416-0.11390.0059-0.03160.06490.01910.02460.0850.010.13691.39698.646446.2292
170.2346-0.17560.34182.5147-1.84471.6436-0.07480.09450.07340.00750.0479-0.1924-0.03740.13430.04670.04680.018-0.00170.1004-0.01330.13986.991510.133548.8428
181.5472-0.35650.31720.96-0.46910.4822-0.3048-0.1730.10690.09190.059-0.0737-0.0808-0.1158-0.47830.01220.0759-0.0340.2186-0.07820.150411.99643.661952.9474
190.8804-0.210.34071.7089-0.74061.5242-0.0702-0.10690.03950.15630.0894-0.0308-0.1341-0.0067-0.01490.05680.0044-0.00620.1218-0.01280.08545.12368.670352.9835
202.0079-1.24021.45361.6232-1.49722.2526-0.3182-0.1528-0.03580.2970.4135-0.06490.444-0.4255-0.05280.3518-0.0094-0.04330.2217-0.02960.286-2.9299-10.522722.3972
210.6695-0.236-0.12210.9932-0.04111.8597-0.0390.0648-0.06480.03420.0567-0.00660.2014-0.0101-0.0450.205-0.023-0.01980.12780.00340.1328-0.6222-6.781812.6914
221.2227-0.8495-0.46781.9014-0.27350.45160.0167-0.06160.04480.00080.00720.00120.0932-0.0601-0.01020.0674-0.0023-0.01770.0950.00610.0961-4.01710.521943.3447
232.114-0.7358-0.3341.9820.34411.4612-0.04610.0971-0.08120.0334-0.05210.23850.1351-0.36460.03930.0673-0.0281-0.00970.14650.00670.1871-12.8939-1.37945.0308
241.2-0.42461.15693.5164-0.02622.34920.001-0.4762-0.09060.60210.11150.30230.0446-0.2303-0.00190.16880.00650.03170.1632-0.03110.137123.011335.043630.8223
252.8003-0.8335-0.5542.2448-0.19822.2367-0.0011-0.43180.1440.5787-0.0733-0.36330.14160.45740.01750.2917-0.0593-0.06760.29470.02320.2068.61294.29928.4616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:25 )A1 - 25
2X-RAY DIFFRACTION2( CHAIN A AND RESID 26:101 )A26 - 101
3X-RAY DIFFRACTION3( CHAIN A AND RESID 102:128 )A102 - 128
4X-RAY DIFFRACTION4( CHAIN A AND RESID 129:150 )A129 - 150
5X-RAY DIFFRACTION5( CHAIN A AND RESID 151:163 )A151 - 163
6X-RAY DIFFRACTION6( CHAIN A AND RESID 164:213 )A164 - 213
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:17 )B1 - 17
8X-RAY DIFFRACTION8( CHAIN B AND RESID 18:130 )B18 - 130
9X-RAY DIFFRACTION9( CHAIN B AND RESID 131:151 )B131 - 151
10X-RAY DIFFRACTION10( CHAIN B AND RESID 152:194 )B152 - 194
11X-RAY DIFFRACTION11( CHAIN B AND RESID 195:220 )B195 - 220
12X-RAY DIFFRACTION12( CHAIN B AND ( RESID 221:221 OR RESID 301:301 ) )B221
13X-RAY DIFFRACTION12( CHAIN B AND ( RESID 221:221 OR RESID 301:301 ) )B301
14X-RAY DIFFRACTION13( CHAIN C AND RESID 1:25 )C1 - 25
15X-RAY DIFFRACTION14( CHAIN C AND RESID 26:75 )C26 - 75
16X-RAY DIFFRACTION15( CHAIN C AND RESID 76:101 )C76 - 101
17X-RAY DIFFRACTION16( CHAIN C AND RESID 102:128 )C102 - 128
18X-RAY DIFFRACTION17( CHAIN C AND RESID 129:150 )C129 - 150
19X-RAY DIFFRACTION18( CHAIN C AND RESID 151:163 )C151 - 163
20X-RAY DIFFRACTION19( CHAIN C AND RESID 164:213 )C164 - 213
21X-RAY DIFFRACTION20( CHAIN D AND RESID 1:17 )D1 - 17
22X-RAY DIFFRACTION21( CHAIN D AND RESID 18:117 )D18 - 117
23X-RAY DIFFRACTION22( CHAIN D AND RESID 118:194 )D118 - 194
24X-RAY DIFFRACTION23( CHAIN D AND ( RESID 195:220 OR RESID 301:301 ) )D195 - 220
25X-RAY DIFFRACTION23( CHAIN D AND ( RESID 195:220 OR RESID 301:301 ) )D301
26X-RAY DIFFRACTION24( CHAIN E AND RESID 1:12 )E1 - 12
27X-RAY DIFFRACTION25( CHAIN F AND RESID 1:12 )F1 - 12

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