5U5F | pdb_00005u5f

MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQFDA(PH)2STRRLRCGGSK

PDB DOI: https://doi.org/10.2210/pdb5U5F/pdb

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

Deposited: 2016-12-06 Released: 2018-03-14
Deposition Author(s): Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Meditope Enabled Trastuzumab I83E Variant In Complex With (Ac)Cqfda(Ph)2Strrlrcggsk

Bzymek, K.P., Avery, K.N., Zer, C., Williams, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 62.41 kDa
Atom Count: 5,342
Modeled Residue Count: 567
Deposited Residue Count: 573
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 FAB LIGHT CHAIN I83E	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 FAB 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]	65	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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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
5-DIPHENYL LONG MEDITOPE	D	17	synthetic construct	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin G binding protein A	E [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

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] mmCIF 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	D	L-PEPTIDE LINKING	C₁₅ H₁₅ N O₂		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.43	α = 90
b = 105.38	β = 90
c = 117	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