6FJ3

High resolution crystal structure of parathyroid hormone 1 receptor in complex with a peptide agonist.

PDB DOI: https://doi.org/10.2210/pdb6FJ3/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Pyrococcus abyssi GE5, Equus caballus
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2018-01-19 Released: 2018-11-21
Deposition Author(s): Ehrenmann, J., Schoppe, J., Klenk, C., Rappas, M., Kummer, L., Dore, A.S., Pluckthun, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248
R-Value Work: 0.209
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 78.58 kDa
Atom Count: 5,352
Modelled Residue Count: 597
Deposited Residue Count: 637
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathyroid hormone/parathyroid hormone-related peptide receptor,Parathyroid hormone/parathyroid hormone-related peptide receptor,GlgA glycogen synthase,Parathyroid hormone/parathyroid hormone-related peptide receptor	A	602	Homo sapiens, Pyrococcus abyssi GE5	Mutation(s): 10 Gene Names: PTH1R, PTHR, PTHR1, PAB2292 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V2J8 Go to UniProtKB: Q9V2J8
Find proteins for Q03431 (Homo sapiens) Explore Q03431 Go to UniProtKB: Q03431
PHAROS: Q03431 GTEx: ENSG00000160801
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q9V2J8Q03431
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathyroid hormone	B	35	Equus caballus	Mutation(s): 5 Gene Names: PTH Membrane Entity: Yes
UniProt
Find proteins for Q27IM2 (Equus caballus) Explore Q27IM2 Go to UniProtKB: Q27IM2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q27IM2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G82348BZ GlyCosmos: G82348BZ GlyGen: G82348BZ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OLA Query on OLA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A]	R [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A]	T [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM Query on YCM	A	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS
AIB Query on AIB	B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
HRG Query on HRG	B	L-PEPTIDE LINKING	C₇ H₁₆ N₄ O₂		ARG
NLE Query on NLE	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		LEU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248
R-Value Work: 0.209
R-Value Observed: 0.211
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.115	α = 80.63
b = 52.864	β = 83.76
c = 111.874	γ = 79.16

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-11-21
Type: Initial release
Version 1.1: 2018-11-28
Changes: Data collection, Database references
Version 1.2: 2018-12-19
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary