BMRB Entry 31146

Name: Pembrolizumab CDR-H3 Loop Mimic
Published: 2024-06-24

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PDB ID: 8w0q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31146
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Pembrolizumab CDR-H3 Loop Mimic

Deposition date:

2024-02-14

Original release date:

2024-06-24

Authors:

Feig, M.; Roche, S.

Citation:

Citation: Zhao, G.; Richaud, A.; Williamson, R.; Feig, M.; Roche, S.. "De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics" ACS Chem. Biol. ., .-..

Assembly members:

Assembly members:
entity_1, polymer, 20 residues, 2667.957 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: RWVARRDYRGDMGFDYWVWE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	79
15N chemical shifts	17
1H chemical shifts	146

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 20 residues - 2667.957 Da.

1		ARG	TRP	VAL	ALA	ARG	ARG	ASP	TYR	ARG	GLY
2		ASP	MET	GLY	PHE	ASP	TYR	TRP	VAL	TRP	GLU

Samples:

sample_1: Hairpin 5.0 mM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 291 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

VnmrJ v4.2, Varian - processing

TopSpin v3.2, Bruker Biospin - processing

CHARMM vc42a2, CHARMM - refinement, structure calculation

MestreLab (Mnova / MestReNova / MestReC) v15.0.0, Mestrelab - peak picking

NMR spectrometers:

Varian Varian Mercury500 500 MHz
Bruker Bruker Neo NMR 500 MHz
Bruker Bruker AVANCE III 700 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1		ARG	TRP	VAL	ALA	ARG	ARG	ASP	TYR	ARG	GLY
2		ASP	MET	GLY	PHE	ASP	TYR	TRP	VAL	TRP	GLU

1		ARG	TRP	VAL	ALA	ARG	ARG	ASP	TYR	ARG	GLY
2		ASP	MET	GLY	PHE	ASP	TYR	TRP	VAL	TRP	GLU

1		ARG	TRP	VAL	ALA	ARG	ARG	ASP	TYR	ARG	GLY
2		ASP	MET	GLY	PHE	ASP	TYR	TRP	VAL	TRP	GLU