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- PDB-5u6a: CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO... -

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Basic information

Entry
Database: PDB / ID: 5u6a
TitleCRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE
Components
  • Heavy Chain
  • Immunoglobulin G binding protein A
  • Light Chain
  • Protein L
  • meditope peptide
KeywordsIMMUNE SYSTEM / ANTIBODY / ANTIBODY-DRUG CONJUGATES
Function / homology
Function and homology information


IgG binding / immunoglobulin binding / extracellular region
Similarity search - Function
Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Octapeptide repeat / Octapeptide repeat ...Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MESO-ERYTHRITOL / Immunoglobulin G-binding protein A / Immunoglobulin G binding protein A / Protein L
Similarity search - Component
Biological speciesHomo sapiens (human)
Finegoldia magna (bacteria)
Staphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.736 Å
AuthorsWilliams, J.C. / Bzymek, K.P. / Pucket, J. / Avery, K.A. / Ma, Y. / Xie, J. / Zer, C. / Horne, D.
CitationJournal: To Be Published
Title: Crystal Structure Of I83E Meditope-Enabled Trastuzumab With Azido-PEG3-Meditope
Authors: Williams, J.C. / Bzymek, K.P. / Pucket, J. / Avery, K.A. / Ma, Y. / Xie, J. / Zer, C. / Horne, D.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / pdbx_struct_assembly_prop / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _entity.pdbx_fragment / _entity_src_gen.gene_src_common_name ..._entity.pdbx_fragment / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 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 1.4Nov 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_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: Light Chain
B: Heavy Chain
E: Protein L
C: Immunoglobulin G binding protein A
D: meditope peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1546
Polymers62,0325
Non-polymers1221
Water15,439857
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-40 kcal/mol
Surface area24090 Å2
Unit cell
Length a, b, c (Å)53.250, 105.170, 117.070
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, 3 molecules ABC

#1: Antibody Light Chain


Mass: 23518.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Heavy Chain


Mass: 23774.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Immunoglobulin G binding protein A


Mass: 6037.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli (E. coli) / References: UniProt: Q2UW42, UniProt: P02976*PLUS

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Protein / Protein/peptide , 2 types, 2 molecules ED

#3: Protein Protein L


Mass: 6850.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918
#5: Protein/peptide meditope peptide


Mass: 1851.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 858 molecules

#6: Chemical ChemComp-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 3350 200 MM NACL, PH 7.2

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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 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.736→31.526 Å / Num. obs: 65702 / % possible obs: 95.6 % / Redundancy: 2.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.6
Reflection shellResolution: 1.736→1.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.24 / Num. unique all: 3974 / CC1/2: 0.79 / % possible all: 76.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ioi
Resolution: 1.736→31.526 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.47
RfactorNum. reflection% reflection
Rfree0.1875 3285 5 %
Rwork0.1594 --
obs0.1609 65699 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.736→31.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 8 857 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074744
X-RAY DIFFRACTIONf_angle_d1.0986489
X-RAY DIFFRACTIONf_dihedral_angle_d11.8932891
X-RAY DIFFRACTIONf_chiral_restr0.053713
X-RAY DIFFRACTIONf_plane_restr0.005859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7361-1.7620.26861050.24851988X-RAY DIFFRACTION71
1.762-1.78950.26061350.23432566X-RAY DIFFRACTION93
1.7895-1.81880.24611470.21832784X-RAY DIFFRACTION99
1.8188-1.85020.25511470.20232790X-RAY DIFFRACTION100
1.8502-1.88380.25091460.19132775X-RAY DIFFRACTION99
1.8838-1.92010.21851470.18232806X-RAY DIFFRACTION99
1.9201-1.95930.22051460.17842774X-RAY DIFFRACTION99
1.9593-2.00190.18931470.16912778X-RAY DIFFRACTION99
2.0019-2.04840.19631480.17182813X-RAY DIFFRACTION99
2.0484-2.09960.19731450.16342768X-RAY DIFFRACTION99
2.0996-2.15640.18781480.1562799X-RAY DIFFRACTION99
2.1564-2.21980.19511480.1562821X-RAY DIFFRACTION99
2.2198-2.29150.18341460.15512765X-RAY DIFFRACTION99
2.2915-2.37330.18451460.15782780X-RAY DIFFRACTION99
2.3733-2.46830.19941470.15972800X-RAY DIFFRACTION99
2.4683-2.58060.23621460.16022773X-RAY DIFFRACTION98
2.5806-2.71660.16311450.15812754X-RAY DIFFRACTION97
2.7166-2.88670.19981440.15722726X-RAY DIFFRACTION96
2.8867-3.10940.20231440.15872746X-RAY DIFFRACTION96
3.1094-3.4220.1821420.14592698X-RAY DIFFRACTION94
3.422-3.91630.15241410.13482669X-RAY DIFFRACTION92
3.9163-4.93110.12271390.1232652X-RAY DIFFRACTION90
4.9311-31.5310.17731360.16932589X-RAY DIFFRACTION85
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)
10.6788-0.0083-0.98994.2188-5.03647.45860.05490.00420.00220.0410.13520.0527-0.26-0.1032-0.22890.13530.0028-0.00160.0955-0.02570.1207-19.317634.2462-10.0221
21.87030.33090.16381.7526-0.69490.94720.0198-0.07140.0815-0.0130.0006-0.1298-0.09220.156-0.03120.0471-0.0104-0.00340.099-0.00680.1022-10.233328.6833-8.2397
30.2214-0.20060.36070.4894-0.63681.56460.01820.0208-0.0033-0.03410.0570.01320.0355-0.0166-0.04180.0672-0.02230.00230.0899-0.00590.0854-21.135526.6762-25.749
44.79323.8492.61883.92642.93322.96570.1105-0.17590.10750.1408-0.06880.17710.1781-0.3094-0.03460.1222-0.0285-0.01080.12170.04440.079-31.554730.7912-38.7358
53.48391.67531.5573.17530.42763.1690.2103-0.1167-0.13220.20940.0103-0.16520.1096-0.1692-0.20950.0924-0.00760.03050.09720.02140.064-28.808629.3917-35.2577
63.24932.34211.70713.74351.84553.00960.1955-0.1416-0.0764-0.17510.01130.45930.3853-0.6270.03260.2087-0.1342-0.11280.25640.08040.195-40.158520.1376-45.0998
73.09483.31293.05165.88452.96094.1035-0.03230.0670.0114-0.32150.21340.31940.1679-0.1849-0.04430.122-0.0427-0.05020.12940.02860.1258-35.310432.7436-47.6955
82.91610.47090.75851.6663-0.00261.9443-0.33730.35350.0512-0.34930.313-0.07660.04670.13720.0240.109-0.00460.00190.0878-0.01770.0923-19.15554.4342-18.0373
93.03270.92830.70841.60510.49152.06520.0429-0.2386-0.2967-0.00670.0074-0.40820.10160.3233-0.13960.0650.0102-0.01080.15590.01730.1947-7.72263.9782-11.1928
102.5706-1.98042.3133.3855-2.30464.52920.0479-0.12230.00250.24530.02810.1019-0.13030.0021-0.08420.0871-0.045-0.01670.0909-0.00580.1109-18.342312.2688-7.668
117.4298-0.60272.09291.1934-0.00592.29130.221-0.49430.13430.2295-0.1766-0.12140.0862-0.1302-0.04320.1649-0.062-0.01320.1150.00940.0962-18.47885.1114-0.2734
122.22181.46371.09152.3299-1.05022.85120.1395-0.1961-0.1450.02530.0139-0.05930.0985-0.0723-0.1490.0917-0.0225-0.0040.049-0.00440.0782-20.17792.0955-10.2275
133.65930.81491.17322.7942-0.00473.7950.0604-0.30920.28510.0868-0.0707-0.4763-0.16630.43690.0590.1004-0.021-0.00270.1537-0.0230.2052-9.428714.8226-9.6011
140.1858-0.4524-0.06011.1235-0.37383.1857-0.13760.06450.0703-0.420.1350.13240.1994-0.2416-0.05260.1712-0.0505-0.03490.10620.03470.1166-27.64326.256-24.3654
150.74680.9123-0.55892.4736-1.68672.71280.0441-0.0466-0.0021-0.1138-0.03130.01820.2151-0.0207-0.01040.1286-0.00630.00590.08580.00790.0848-23.532918.8752-40.5873
162.45381.9556-2.48993.0528-2.09144.1226-0.17350.0679-0.2419-0.72040-0.12390.76110.07050.17730.30850.01070.03630.125-0.00210.1399-19.89511.7836-45.7978
173.67573.4844-1.76733.52-1.0515.4814-0.03220.2743-0.1511-0.26470.1598-0.1561-0.25-0.5251-0.0990.1480.04970.02570.15350.01430.3229-25.197544.4551-15.2878
183.25622.7766-4.02313.1718-2.7715.488-0.14990.33170.4272-0.0810.18810.4393-0.0853-0.7890.1460.11930.00450.00650.17240.00080.1974-26.493539.5537-14.5734
193.70130.8241-1.45393.8760.13722.68540.1115-0.38990.4540.1216-0.03430.0223-0.371-0.2288-0.06790.18260.05330.0140.1887-0.07620.1914-25.63545.5377-6.9186
205.35723.89211.40785.17910.32783.99060.0449-0.12280.2953-0.08050.194-0.1095-0.5111-0.1465-0.19130.26440.06470.09420.1455-0.03860.2925-25.275949.4564-12.4407
216.1544-0.94784.86943.6971-0.01216.76050.1683-0.26690.0290.4778-0.1776-0.37950.26570.43690.01380.2202-0.0116-0.01130.19970.04230.15-24.1768-13.93291.8572
225.05353.74741.32823.53750.90422.48450.2217-0.0724-0.18630.2997-0.1396-0.07360.0560.0958-0.0910.11150.0046-0.00760.05860.02630.1009-27.6179-8.5643-7.5756
233.66980.93384.73023.61271.17936.61470.3063-0.32760.13410.539-0.33770.3871-0.16080.03240.03640.2317-0.05590.05870.16280.00110.1214-31.9618-3.6266-1.568
244.7333-2.1919-1.37884.07351.75263.90180.03270.2124-0.0216-0.2034-0.05870.24540.0426-0.32220.04840.1683-0.0322-0.05740.12760.01190.1479-24.986921.9179-21.6862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 128 )
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 188 )
7X-RAY DIFFRACTION7chain 'A' and (resid 189 through 214 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 32 )
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 52 )
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 67 )
12X-RAY DIFFRACTION12chain 'B' and (resid 68 through 91 )
13X-RAY DIFFRACTION13chain 'B' and (resid 92 through 110 )
14X-RAY DIFFRACTION14chain 'B' and (resid 111 through 126 )
15X-RAY DIFFRACTION15chain 'B' and (resid 127 through 195 )
16X-RAY DIFFRACTION16chain 'B' and (resid 196 through 223 )
17X-RAY DIFFRACTION17chain 'E' and (resid 19 through 33 )
18X-RAY DIFFRACTION18chain 'E' and (resid 34 through 42 )
19X-RAY DIFFRACTION19chain 'E' and (resid 43 through 72 )
20X-RAY DIFFRACTION20chain 'E' and (resid 73 through 81 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 16 )
22X-RAY DIFFRACTION22chain 'C' and (resid 17 through 35 )
23X-RAY DIFFRACTION23chain 'C' and (resid 36 through 54 )
24X-RAY DIFFRACTION24chain 'D' and (resid 0 through 13 )

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