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- PDB-6azl: Structure of cetuximab with aminoheptanoic acid-linked N-carboxye... -

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Basic information

Entry
Database: PDB / ID: 6azl
TitleStructure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope variant
Components
  • cetuximab Fab heavy chain
  • cetuximab Fab light chain
  • meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / 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 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / IgG H chain
Similarity search - Component
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: 2017
Title: Meditope-Fab interaction: threading the hole.
Authors: Bzymek, K.P. / Ma, Y. / Avery, K.N. / Horne, D.A. / Williams, J.C.
History
DepositionSep 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _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: cetuximab Fab light chain
B: cetuximab Fab heavy chain
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
E: meditope
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,2449
Polymers96,9566
Non-polymers2883
Water7,764431
1
A: cetuximab Fab light chain
B: cetuximab Fab heavy chain
E: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5744
Polymers48,4783
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-43 kcal/mol
Surface area18570 Å2
MethodPISA
2
C: cetuximab Fab light chain
D: cetuximab Fab heavy chain
F: meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6705
Polymers48,4783
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-49 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.570, 83.050, 212.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody cetuximab Fab light chain


Mass: 23287.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric murine/human antibody; purified from Erbitux
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: unidentified (others) / References: UniProt: P01834
#2: Antibody cetuximab Fab heavy chain


Mass: 23725.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: chimeric murine/human antibody; purified from Erbitux
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: unidentified (others) / References: UniProt: S6B291
#3: Protein/peptide meditope


Mass: 1464.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light ...Sequence of cetuximab Fab light chain in this entry matches to the sequence of cetuximab Fab light chain from the first deposited cetuximab structure in PDB (1yy8)

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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: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citrate pH 5.5, 1.8 M ammonium sulfate

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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 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→33.173 Å / Num. obs: 40967 / % possible obs: 99.3 % / Redundancy: 5.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 42.3
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 14 / Num. unique obs: 2746 / CC1/2: 0.99 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.482→33.173 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.88
RfactorNum. reflection% reflection
Rfree0.2158 2048 5 %
Rwork0.1695 --
obs0.1718 40961 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.482→33.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6724 0 15 431 7170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086940
X-RAY DIFFRACTIONf_angle_d1.1689457
X-RAY DIFFRACTIONf_dihedral_angle_d10.9224135
X-RAY DIFFRACTIONf_chiral_restr0.0791064
X-RAY DIFFRACTIONf_plane_restr0.0051210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4815-2.53920.30211220.20772318X-RAY DIFFRACTION91
2.5392-2.60270.24691370.18292589X-RAY DIFFRACTION100
2.6027-2.6730.24341340.17362559X-RAY DIFFRACTION100
2.673-2.75160.24561350.18022562X-RAY DIFFRACTION100
2.7516-2.84040.24871360.17872589X-RAY DIFFRACTION100
2.8404-2.94190.24521360.18882573X-RAY DIFFRACTION100
2.9419-3.05960.25711350.18992580X-RAY DIFFRACTION100
3.0596-3.19870.26591370.1932602X-RAY DIFFRACTION100
3.1987-3.36720.2191360.1772579X-RAY DIFFRACTION100
3.3672-3.5780.23941370.15762609X-RAY DIFFRACTION100
3.578-3.85380.19211370.1582600X-RAY DIFFRACTION100
3.8538-4.24090.17261390.14162632X-RAY DIFFRACTION100
4.2409-4.8530.15881390.12972639X-RAY DIFFRACTION100
4.853-6.1080.19221410.15772675X-RAY DIFFRACTION100
6.108-33.17640.20841470.21022807X-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)
10.4009-0.0238-0.35030.1503-0.0490.28520.0605-0.07950.0381-0.08350.1348-0.2520.22830.24330.01460.22750.0328-0.05070.19840.01140.11-19.475623.6096-19.4194
20.2935-0.1185-0.32180.52170.39020.44350.00820.1084-0.07680.0915-0.00240.05880.08580.0181-00.1857-0.0117-0.04480.16640.04080.0987-28.232726.3381-13.4153
30.1249-0.077-0.01790.1095-0.0220.01630.06380.0771-0.13430.0235-0.0761-0.15450.0855-0.0463-00.2091-0.0167-0.02280.1798-0.01090.136-28.280823.9942-21.7019
40.2845-0.092-0.26830.10540.38750.4591-0.0076-0.06190.01330.05260.02880.02130.0007-0.10110.00050.1306-0.003-0.02570.06720.04540.1069-28.173931.4922-37.0266
50.1024-0.00820.01420.12410.05150.22310.04210.0037-0.1117-0.03440.02130.0571-0.00690.121200.088-0.0008-0.02040.14060.050.2037-24.90427.2138-50.933
60.0265-0.03390.01230.0499-0.05770.0420.00690.0901-0.1003-0.0449-0.0398-0.06330.0547-0.058800.098-0.0216-0.01840.1827-0.02690.2022-20.100633.606-55.7591
70.5653-0.10880.01570.57450.17980.25820.02470.1158-0.0374-0.103-0.0045-0.007-0.04330.0779-00.12660.0111-0.00190.14130.04790.1637-26.808228.2593-54.8807
80.00970.0147-0.00730.21190.20640.1883-0.2003-0.22580.1978-0.04250.11680.1665-0.2881-0.1347-0.0010.1597-0.0281-0.01060.24730.01320.1849-38.796547.9235-20.1624
90.18990.12050.41050.0150.02630.6969-0.0029-0.04590.01580.03180.00260.0329-0.14860.096400.1756-0.02310.01260.15040.02160.1396-31.881346.9308-19.5898
100.2296-0.02510.07920.00270.01710.28410.0065-0.0365-0.3244-0.1794-0.0174-0.1714-0.049-0.015600.1232-0.0112-0.0090.1188-0.01230.2397-37.42230.8791-52.8069
110.0574-0.1239-0.06910.411-0.06370.61540.0224-0.09190.1260.0728-0.09270.12860.0413-0.025500.0687-0.0162-0.01440.10550.02490.1871-36.480635.4529-43.6504
120.3041-0.09330.03030.0408-0.06930.17-0.0425-0.11090.0263-0.0443-0.04320.1883-0.0245-0.15900.115-0.0046-0.00850.108-0.03380.196-45.288638.5661-47.4459
130.17760.01690.18450.07150.08690.1924-0.0252-0.14760.0818-0.1473-0.07420.0023-0.1348-0.1148-00.1960.0269-0.00420.18810.00590.1929-11.713516.975-18.245
140.4067-0.04660.41910.4239-0.22330.50170.13030.01030.0797-0.07440.0820.027-0.32060.05410.00070.21450.01480.01110.1495-0.01930.091-3.102314.2376-11.8558
150.2082-0.14160.3485-0.0379-0.24450.4732-0.0005-0.0031-0.02190.06220.0383-0.0267-0.1313-0.0794-0.00050.2095-0.00910.02170.0825-0.00360.1133-3.85739.8133-30.3155
160.08260.1303-0.01990.12080.06830.24240.0268-0.04520.0533-0.07020.10070.02770.06190.0062-00.0918-0.00080.00890.0998-0.01290.207-7.081610.1287-48.955
170.1375-0.0262-0.14580.7782-0.02020.15590.09240.1497-0.0089-0.01470.13910.1450.0470.27890.08220.0806-0.0173-0.03630.19520.01790.1787-12.12183.6194-53.0506
180.77050.1299-0.05140.41220.02580.4932-0.09560.12030.0134-0.05450.1093-0.0057-0.04530.1238-00.1178-0.0069-0.04210.1492-0.00680.1251-5.42348.7243-52.9158
190.03690.34530.16010.3640.07150.8265-0.0734-0.0157-0.0248-0.010.12210.03180.14070.067100.20190.0201-0.01150.1524-0.00780.13041.135-7.0409-13.8715
200.301-0.1325-0.11360.19360.41480.966-0.08930.0850.20240.04380.0187-0.11850.43370.1036-0.04780.04270.01170.04230.06820.02590.19633.0711-5.0418-45.7558
210.01120.1715-0.15970.6692-0.17530.68380.0083-0.042-0.0480.0019-0.0236-0.04020.05470.102800.1027-0.0076-0.01790.1225-0.03240.16957.21750.809-43.3921
220.03330.02240.04180.03920.01970.05850.1424-0.12660.2008-0.50140.03440.2344-0.0312-0.0540.00120.1470.0081-0.00320.23250.03680.214-26.203736.3287-30.7885
230.0681-0.1411-0.04670.28090.09930.04160.2368-0.17820.1573-0.48760.01830.03440.2597-0.14140.01670.15880.0017-0.05730.2421-0.01470.1822-5.44132.74-28.1088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1:25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26:75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76:90 )
4X-RAY DIFFRACTION4chain 'A' and (resid 91:128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129:150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 151:163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164:212 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1:33 )
9X-RAY DIFFRACTION9chain 'B' and (resid 34:130 )
10X-RAY DIFFRACTION10chain 'B' and (resid 131:151 )
11X-RAY DIFFRACTION11chain 'B' and (resid 152:194 )
12X-RAY DIFFRACTION12chain 'B' and (resid 195:220 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1:25 )
14X-RAY DIFFRACTION14chain 'C' and (resid 26:75 )
15X-RAY DIFFRACTION15chain 'C' and (resid 76:128 )
16X-RAY DIFFRACTION16chain 'C' and (resid 129:150 )
17X-RAY DIFFRACTION17chain 'C' and (resid 151:163 )
18X-RAY DIFFRACTION18chain 'C' and (resid 164:212 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1:117 )
20X-RAY DIFFRACTION20chain 'D' and (resid 118:140 )
21X-RAY DIFFRACTION21chain 'D' and (resid 141:220 )
22X-RAY DIFFRACTION22chain 'E' and (resid 2:11 )
23X-RAY DIFFRACTION23chain 'F' and (resid 2:11 )

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