5U5M

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-MEDITOPE

PDB DOI: https://doi.org/10.2210/pdb5U5M/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Finegoldia magna, Staphylococcus aureus, synthetic construct
Expression System: Cricetulus griseus, Escherichia coli
Mutation(s): Yes

Deposited: 2016-12-06 Released: 2018-03-14
Deposition Author(s): Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.197
R-Value Work: 0.161
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure Of I83E Meditope-Enabled Trastuzumab With Azido-Meditope

Williams, J.C., Bzymek, K.P., Pucket, J., Avery, K.A., Ma, Y., Xie, J., Zer, C., Horne, D.

To be published.

Macromolecule Content

Total Structure Weight: 62.14 kDa
Atom Count: 5,221
Modelled Residue Count: 567
Deposited Residue Count: 567
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMAB TRASTUZUMAB, LIGHT CHAIN	A	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MEMAB TRASTUZUMAB, HEAVY CHAIN	B	223	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein L	C [auth E]	63	Finegoldia magna	Mutation(s): 5
UniProt
Find proteins for Q51918 (Finegoldia magna) Explore Q51918 Go to UniProtKB: Q51918
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q51918
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G binding protein A	D [auth C]	54	Staphylococcus aureus	Mutation(s): 0 Gene Names: spa
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P02976 Go to UniProtKB: P02976
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02976
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AZIDO-PEG4-MEDITOPE	E [auth D]	13	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRY Query on MRY Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	MESO-ERYTHRITOL C₄ H₁₀ O₄ UNXHWFMMPAWVPI-ZXZARUISSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2GX Query on 2GX	E [auth D]	L-PEPTIDE LINKING	C₁₅ H₁₅ N O₂		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.197
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.53	α = 90
b = 105.47	β = 90
c = 117.13	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-03-28
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.2: 2018-04-18
Changes: Data collection
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection, Derived calculations