1AXI: STRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE

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Data API 1AXI | pdb_00001axi

STRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE

• PDB DOI: https://doi.org/10.2210/pdb1AXI/pdb

• Classification: COMPLEX (HORMONE/RECEPTOR)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Deposited: 1997-10-15 Released: 1998-01-28 
• Deposition Author(s): Atwell, S., Ultsch, M., De Vos, A.M., Wells, J.A.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.190 (Depositor) 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Structural plasticity in a remodeled protein-protein interface.

Atwell, S., Ultsch, M., De Vos, A.M., Wells, J.A.

(1997) Science 278: 1125-1128

• PubMed: 9353194 Search on PubMed
• DOI: https://doi.org/10.1126/science.278.5340.1125
• Primary Citation of Related Structures:  1AXI
• PubMed Abstract: 

  Remodeling of the interface between human growth hormone (hGH) and the extracellular domain of its receptor was studied by deleting a critical tryptophan residue (at position 104) in the receptor, creating a large cavity, and selecting a pentamutant of hGH by phage display that fills the cavity and largely restores binding affinity. A 2.1 A resolution x-ray structure of the mutant complex showed that the receptor cavity was filled by selected hydrophobic mutations of hGH. Large structural rearrangements occurred in the interface at sites that were distant from the mutations. Such plasticity may be a means for protein-protein interfaces to adapt to mutations as they coevolve.

   View More
Organizational Affiliation: 
• Department of Protein Engineering, Genentech, Incorporated, 460 Point San Bruno Boulevard, South San Francisco, CA 94080, USA.

Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (SO4)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (SO4)

Global Symmetry: Cyclic - C2 (Explore in 3D)Global Stoichiometry: Hetero 4-mer - A2B2 LessFind Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

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Macromolecule Content 

• Total Structure Weight: 49.35 kDa 
• Atom Count: 3,321 
• Modeled Residue Count: 366 
• Deposited Residue Count: 427 
• Unique protein chains: 2

MacromoleculesFind similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GROWTH HORMONE	A	191	Homo sapiens	Mutation(s): 6
UniProt & NIH Common Fund Data Resources
Find proteins for P01241 (Homo sapiens)Explore P01241 Go to UniProtKB:  P01241
PHAROS:  P01241GTEx:  ENSG00000259384
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01241
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GROWTH HORMONE RECEPTOR	B	236	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P10912 (Homo sapiens)Explore P10912 Go to UniProtKB:  P10912
PHAROS:  P10912GTEx:  ENSG00000112964
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10912
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4Query on SO4Download Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE IONO4 SQAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.262 (Depositor) 
• R-Value Work:  0.190 (Depositor) 

Space Group: P 43 21 2Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.6	α = 90
b = 65.6	β = 90
c = 231.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
REFMAC	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Atwell, S., Ultsch, M., De Vos, A.M., Wells, J.A.

Revision History (Full details and data files)

• Version 1.0: 1998-01-28Type: Initial release
• Version 1.1: 2008-03-24Changes: Version format compliance
• Version 1.2: 2011-07-13Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-03Changes: Database references, Derived calculations
• Version 1.4: 2024-04-03Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20Changes: Structure summary

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