6BGT | pdb_00006bgt

Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain

PDB DOI: https://doi.org/10.2210/pdb6BGT/pdb

Classification: TRANSFERASE/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-10-29 Released: 2018-10-31
Deposition Author(s): Christie, M., Christ, D.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.247 (Depositor), 0.246 (DCC)
R-Value Work:
0.205 (Depositor), 0.208 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Stable human IgG antibody therapeutics with native framework structure

Christie, M., Rouet, R., Nevoltris, D., Langley, D., Schofield, P., Fabri, L., Tingly, K., Lowe, D., Jermutus, L., Christ, D.

To be published.

Macromolecule Content

Total Structure Weight: 120.92 kDa
Atom Count: 7,806
Modeled Residue Count: 1,010
Deposited Residue Count: 1,103
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	A [auth C]	658	Homo sapiens	Mutation(s): 0 Gene Names: ERBB2, HER2, MLN19, NEU, NGL EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04626 (Homo sapiens) Explore P04626 Go to UniProtKB: P04626
PHAROS: P04626 GTEx: ENSG00000141736
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04626
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth C]	Go to GlyGen: P04626-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Herceptin light chain mutant	B [auth A]	214	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q7Z3Y4 (Homo sapiens) Explore Q7Z3Y4 Go to UniProtKB: Q7Z3Y4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7Z3Y4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Herceptin heavy chain Fab fragment mutant	C [auth B]	231	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5 Go to UniProtKB: P0DOX5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DOX5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth C] MOL2 format, chain D [auth C] mmCIF format, chain D [auth C]	D [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.247 (Depositor), 0.246 (DCC)
R-Value Work: 0.205 (Depositor), 0.208 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.86	α = 90
b = 114.46	β = 90
c = 204.279	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Christie, M.

Christ, D.

Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DE160100608
Australian Research Council (ARC)	Australia	DP160104915

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-23
Changes: Structure summary