2QKH

Crystal structure of the extracellular domain of human GIP receptor in complex with the hormone GIP

PDB DOI: https://doi.org/10.2210/pdb2QKH/pdb

Classification: SIGNALING PROTEIN/HORMONE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2007-07-11 Released: 2007-08-14
Deposition Author(s): Parthier, C., Kleinschmidt, M., Neumann, P., Rudolph, R., Manhart, S., Schlenzig, D., Fanghanel, J., Rahfeld, J.-U., Demuth, H.-U., Stubbs, M.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.183
R-Value Work: 0.166
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 21.78 kDa
Atom Count: 1,250
Modelled Residue Count: 126
Deposited Residue Count: 177
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-dependent insulinotropic polypeptide	A [auth B]	42	N/A	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P09681 (Homo sapiens) Explore P09681 Go to UniProtKB: P09681
PHAROS: P09681 GTEx: ENSG00000159224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09681
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-dependent insulinotropic polypeptide receptor	B [auth A]	135	Homo sapiens	Mutation(s): 0 Gene Names: GIPR Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P48546 (Homo sapiens) Explore P48546 Go to UniProtKB: P48546
PHAROS: P48546 GTEx: ENSG00000010310
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P48546
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cyclic 2,3-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-2,6-di-O-methyl-alpha-D-glucopyranose-(1-4)-2-O-methyl-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-3-O-methyl-alpha-D-glucopyranose	C	7		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G04274SM GlyCosmos: G04274SM

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAR Query on TAR Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900086 Query on PRD_900086	C	methyl-beta-cyclodextrin	Oligosaccharide / Drug delivery		Interactions Focus chain C Interactions & Density Focus chain C

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.183
R-Value Work: 0.166
R-Value Observed: 0.167
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.007	α = 90
b = 84.007	β = 90
c = 180.947	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
SHELXS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-08-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-18
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary