[English] 日本語
Yorodumi
- PDB-5hpm: Cetuximab Fab in complex with cyclic linked meditope -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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)

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more