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- PDB-5hpm: Cetuximab Fab in complex with cyclic linked meditope -

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Basic information

Entry
Database: PDB / ID: 5hpm
TitleCetuximab Fab in complex with cyclic linked meditope
Components
  • (Cetuximab Fab ...) x 2
  • N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-AMINO-3-MERCAPTO-PROPIONAMIDE
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Ma, Y. / Avery, K.A. / Horne, D.A. / Williams, J.C.
History
DepositionJan 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 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 1.3Sep 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 2.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / struct_conn / struct_ref_seq / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id

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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: N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope
F: N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,50010
Polymers96,8186
Non-polymers6834
Water5,026279
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7505
Polymers48,4093
Non-polymers3412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-31 kcal/mol
Surface area18770 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7505
Polymers48,4093
Non-polymers3412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-32 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.110, 82.760, 212.680
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, 4 molecules EF

#3: Protein/peptide N-ACETYL-L-CYSTEINE, Cyclic amidated, acetylated linked meditope


Mass: 1395.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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, 281 molecules

#5: Chemical ChemComp-CY3 / 2-AMINO-3-MERCAPTO-PROPIONAMIDE


Type: L-peptide linking / Mass: 120.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8N2OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate, 0.1 M sodium phosphate dibasic, 0.5 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic

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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: Dec 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.67→33.05 Å / Num. obs: 32836 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.218 / Net I/σ(I): 8.85
Reflection shellResolution: 2.67→2.74 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.91 / % possible all: 100

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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: 2.67→33.046 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.19
RfactorNum. reflection% reflection
Rfree0.2323 1641 5 %
Rwork0.1874 --
obs0.1897 32826 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.67→33.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 0 279 7043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036949
X-RAY DIFFRACTIONf_angle_d0.6199470
X-RAY DIFFRACTIONf_dihedral_angle_d11.7364154
X-RAY DIFFRACTIONf_chiral_restr0.0451074
X-RAY DIFFRACTIONf_plane_restr0.0041214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6699-2.74840.33341320.25472518X-RAY DIFFRACTION100
2.7484-2.8370.30061340.25192550X-RAY DIFFRACTION100
2.837-2.93840.33691360.25622577X-RAY DIFFRACTION100
2.9384-3.0560.28641360.22712589X-RAY DIFFRACTION100
3.056-3.19490.26771360.20582572X-RAY DIFFRACTION100
3.1949-3.36320.22531360.19232581X-RAY DIFFRACTION100
3.3632-3.57370.20261360.18232592X-RAY DIFFRACTION100
3.5737-3.84920.21361370.17212593X-RAY DIFFRACTION100
3.8492-4.23590.21731370.15142612X-RAY DIFFRACTION100
4.2359-4.84720.1761380.12932620X-RAY DIFFRACTION100
4.8472-6.10070.18831400.16252662X-RAY DIFFRACTION100
6.1007-33.04810.23141430.20772719X-RAY DIFFRACTION97
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)
11.28210.0301-0.66311.9963-0.27532.08640.07830.1589-0.1813-0.09240.09180.05030.3789-0.0949-0.17980.24920.0013-0.05320.1837-0.03830.1754-7.019325.43315.4176
21.3852-0.20450.3993.813-1.98874.29380.20690.4248-0.66970.07780.0168-0.02360.39230.5509-0.13260.23470.0746-0.05370.2016-0.01240.2595-4.02223.959621.862
30.15430.27270.05051.6070.55120.21150.140.3488-0.0784-0.540.3680.38010.0629-0.4028-0.26350.30520.0258-0.07090.21260.04190.1607-10.339538.35159.8122
40.7834-0.4199-0.02550.7253-0.92862.15970.001-0.09180.0537-0.08960.1115-0.0257-0.12810.3234-0.05810.1457-0.04040.04750.1650.01540.2071-1.961728.22448.1529
51.2955-0.8254-0.6673.32262.64172.7624-0.08150.07450.4207-0.27870.04790.4332-0.0757-0.20720.09220.07060.04120.00440.2251-0.07050.3295-7.479627.129950.9992
63.3158-1.1208-1.64241.25261.65732.3546-0.1415-0.2028-0.43740.0347-0.03280.2447-0.1189-0.55430.08150.16220.07310.00420.270.02210.3132-12.324833.518555.8077
71.58690.9151-0.9792.26340.98423.15980.0337-0.21630.08920.1881-0.22170.2439-0.1483-0.00950.18340.11460.0179-0.02010.177-0.01440.25-5.47628.278255.2132
83.0034-2.273-4.47045.12885.10957.9090.3746-0.07410.3471-0.0240.0128-0.3086-0.64520.3046-0.29250.29890.0070.04720.28280.00460.24142.8250.117926.5564
90.40830.04350.22270.2474-0.60384.2023-0.010.08780.0489-0.07340.0374-0.0201-0.25190.0217-0.03580.16460.00250.02910.1424-0.02170.18521.159945.998420.3084
100.9519-0.52530.27333.1306-0.35991.3297-0.01540.0359-0.04510.0030.06730.090.0270.0221-0.00180.08820.00490.00120.1318-0.01270.18174.238835.403445.0984
115.1242-3.82612.35964.2664-1.14883.3-0.08250.2164-0.17530.03170.08730.0206-0.03360.31870.13580.1148-0.04660.00310.14220.00030.245612.790338.98547.3287
124.1539-4.1771-3.52885.08394.07456.6450.32380.23130.38240.0317-0.0581-0.2248-0.138-0.0053-0.15370.2532-0.0901-0.01260.2309-0.01910.2706-20.393716.725319.2764
131.04080.57220.62512.8093-0.38374.10110.0578-0.04520.20890.00740.23650.1099-0.2898-0.1494-0.26080.18870.00090.00360.19620.0120.1508-28.016914.515612.0664
140.511-0.0384-0.01680.06350.26892.0736-0.01020.03440.0733-0.12180.03020.0254-0.07170.0116-0.0610.2036-0.02280.00260.1640.02260.1434-28.41359.854130.6226
150.5857-0.72860.73713.9564-3.09352.4633-0.13320.1826-0.10580.20880.0837-0.1482-0.20080.01620.12720.1350.01220.05290.14340.00350.2246-25.019510.138348.9272
162.2523-1.1981.68832.0379-1.89621.9925-0.23560.07510.22350.02020.0417-0.0859-0.0771-0.00320.21070.1563-0.0324-0.00370.1513-0.02890.2005-25.08199.396544.9586
171.07240.11010.15335.7871-2.27623.4027-0.0251-0.15320.11090.5761-0.0465-0.0284-0.26830.04920.05720.09520.0367-0.02730.2817-0.04880.158-25.74686.629157.969
183.5541-1.68683.50482.1487-2.38235.4936-0.0718-0.00410.0787-0.24230.0359-0.09830.4139-0.32520.0130.246-0.07830.03120.33830.00630.1996-38.5717-8.447516.7552
191.65151.50581.01733.57453.19875.32150.0026-0.0623-0.2313-0.02420.3644-0.30520.29120.0622-0.27270.2182-0.0191-0.00930.14890.00180.2132-27.388-3.774114.5719
205.02832.27630.48052.97990.30753.4419-0.12290.0832-0.0548-0.04480.0887-0.16510.66910.1460.02510.2910.03830.01120.17420.02620.2667-30.1948-11.60917.1307
210.94330.13830.6146-0.0487-0.19212.70530.02240.1531-0.1302-0.1020.001-0.00210.22720.0814-0.03330.2248-0.00490.01030.12350.00660.2201-33.7768-5.838521.7547
220.7131-0.2624-0.71011.66430.15150.79090.01480.0785-0.00170.0539-0.04610.02520.0754-0.03490.05330.0980.0135-0.02610.1432-0.0120.1866-36.2242.039642.3964
232.4784-1.6033-1.74743.41321.42653.36910.09860.2334-0.00510.0487-0.16680.29150.1629-0.5070.01980.1142-0.0048-0.01940.17210.04410.1942-44.9113-1.327345.0608
247.01990.31330.94592.89541.70016.4201-0.3055-0.4183-0.07450.66390.01510.49430.0551-0.50.18210.2147-0.0072-0.04260.243-0.02850.1914-8.759734.807630.8947
254.8451-0.7181.1425.13520.10624.04810.7769-0.04380.00221.1504-0.4021-0.3391-0.02360.621-0.32110.3333-0.0464-0.07940.2592-0.00540.252-23.84524.368128.3356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'A' and (resid 76 through 90 )
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 128 )
5X-RAY DIFFRACTION5chain 'A' and (resid 129 through 150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 213 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 140 )
10X-RAY DIFFRACTION10chain 'B' and (resid 141 through 195 )
11X-RAY DIFFRACTION11chain 'B' and (resid 196 through 220 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 18 )
13X-RAY DIFFRACTION13chain 'C' and (resid 19 through 75 )
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 128 )
15X-RAY DIFFRACTION15chain 'C' and (resid 129 through 150 )
16X-RAY DIFFRACTION16chain 'C' and (resid 151 through 174 )
17X-RAY DIFFRACTION17chain 'C' and (resid 175 through 213 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 33 )
19X-RAY DIFFRACTION19chain 'D' and (resid 34 through 51 )
20X-RAY DIFFRACTION20chain 'D' and (resid 52 through 72 )
21X-RAY DIFFRACTION21chain 'D' and (resid 73 through 140 )
22X-RAY DIFFRACTION22chain 'D' and (resid 141 through 194 )
23X-RAY DIFFRACTION23chain 'D' and (resid 195 through 220 )
24X-RAY DIFFRACTION24chain 'E' and (resid 1 through 11 )
25X-RAY DIFFRACTION25chain 'F' and (resid 1 through 11 )

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