Macromolecule Content

Total Structure Weight: 41.78 kDa
Atom Count: 2788
Modelled Residue Count: 337
Deposited Residue Count: 372
Unique protein chains: 2

6LBX

Crystal structure of HER2 Domain IV and Rb-H2

DOI: 10.2210/pdb6LBX/pdb

Classification: PROTEIN BINDING
Organism(s): Cyclostomata, Homo sapiens
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): No

Deposited: 2019-11-15 Released: 2020-11-18
Deposition Author(s): Cho, H.S., Cha, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Computationally-guided design and affinity improvement of a protein binder targeting a specific site on HER2

Kim, T.Y., Cha, J.S., Kim, H., Choi, Y., Cho, H.S., Kim, H.S.

(2021) Comput Struct Biotechnol J 19: 1325-1334

DOI: 10.1016/j.csbj.2021.02.013

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Repebody (Rb-H2)	A	275	Cyclostomata	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor tyrosine-protein kinase erbB-2	B	97	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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B]	C [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.228
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.659	α = 90
b = 80.071	β = 90
c = 108.406	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2019-11-15
Released Date: 2020-11-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-11-18
Type: Initial release
Version 1.1: 2021-03-24
Changes: Database references

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.