1kf9

PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 19–256 Chain C； UniProt 19–256	Not recorded	PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；pH 6.30	Resolution 2.60 Å R-free 0.326
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 19–256 Chain F； UniProt 19–256	Not recorded	PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.3；pH 6.30	Resolution 2.60 Å R-free 0.326

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1KF9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A22 HUMAN GROWTH HORMONE BOUND TO SINGLE RECEPTOR Deposited 1998-01-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 19–256（238 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å
1A22 HUMAN GROWTH HORMONE BOUND TO SINGLE RECEPTOR Deposited 1998-01-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 19–256（238 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.60 Å
1AXI STRUCTURAL PLASTICITY AT THE HGH:HGHBP INTERFACE Deposited 1997-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 19–254（236 aa） Fragment：EXTRACELLULAR BINDING DOMAIN	Mutation：W104A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions streak seeding；pH 6.5；CRYSTALLIZED BY STREAK SEEDING AT 5MG/ML COMPLEX IN 50MM BIS-TRIS (PH 6.5) 20% SATURATED AMMONIUM SULFATE, streak seeding	Resolution 2.10 Å R-free 0.262
1HWG 1:2 COMPLEX OF HUMAN GROWTH HORMONE WITH ITS SOLUBLE BINDING PROTEIN Deposited 1996-11-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–255（237 aa） Fragment：EXTRACELLULAR DOMAIN Chain C 19–255（237 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；THE PROTEIN COMPLEX WAS CRYSTALLISED AT PH 6.5 USING 45% (W/V) LISO4 WITH 2% PEG-500 DME AND SOAKED TO PH 5.5 PRIOR TO DATA COLLECTION	Resolution 2.50 Å R-free 0.287
1HWH 1:1 COMPLEX OF HUMAN GROWTH HORMONE MUTANT G120R WITH ITS SOLUBLE BINDING PROTEIN Deposited 1996-11-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 19–255（237 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.75；THE PROTEIN COMPLEX WAS CRYSTALLISED FROM 1.6 M LISO4 AND 50 MM BIS TRIS AT PH 6.75	Resolution 2.90 Å R-free 0.317
2AEW A model for growth hormone receptor activation based on subunit rotation within a receptor dimer Deposited 2005-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 47–251（205 aa） Fragment：residues 29-233	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.70 Å R-free 0.302
2AEW A model for growth hormone receptor activation based on subunit rotation within a receptor dimer Deposited 2005-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 47–251（205 aa） Fragment：residues 29-233	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；PEG, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.70 Å R-free 0.302
3HHR HUMAN GROWTH HORMONE AND EXTRACELLULAR DOMAIN OF ITS RECEPTOR: CRYSTAL STRUCTURE OF THE COMPLEX Deposited 1993-12-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 50–255（206 aa） Chain C 50–254（205 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
5OEK Putative active dimeric state of GHR transmembrane domain Deposited 2017-07-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–294（41 aa） Chain B 254–294（41 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；313 K；Ionic strength (raw mmCIF value) 40；Pressure AMBIENT NMR sample composition 0.7 mM [U-99% 13C; U-99% 15N] GHRtm, 1.2 mM GHRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5OHD Putative inactive (dormant) dimeric state of GHR transmembrane domain Deposited 2017-07-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 254–294（41 aa） Chain B 254–294（41 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；313 K；Ionic strength (raw mmCIF value) 40；Pressure AMBIENT NMR sample composition 0.7 mM [U-99% 13C; U-99% 15N] GHRtm, 1.2 mM GHRtm, 100 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] GHRtm, 50 mM [U-99% 2H] DPC, 0.3 mM sodium azide, 8 mM TCEP, 10 mM citric acid, 20 mM Na2HPO4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GHR_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 19–256 Author chain C； PDBConstruct 1–238； UniProt 19–256 Author chain E； PDBConstruct 1–238； UniProt 19–256 Author chain F； PDBConstruct 1–238； UniProt 19–256

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1kf9
Deposition date deposition_date	2001-11-19
Structure title title	PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR
Keywords keywords	;CYTOKINE, HORMONE-RECEPTOR COMPLEX, PHAGE DISPLAY MOLECULAR PLASTICITY, RECEPTOR HOMODIMERIZATION, HUMAN GROWTH HORMONE, HORMONE-GROWTH FACTOR COMPLEX ;; HORMONE/GROWTH FACTOR
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	37.29 Å
Radius of gyration Rg (electron density) rg_electron	37.27 Å
Forward intensity I(0) i0	220482000.00
Molecular weight molecular_weight	122030.0 kDa
Excluded volume excluded_volume	153270 Å³
Envelope volume envelope_volume	201030 Å³
Hydration-shell volume shell_volume	46727 Å³
Envelope diameter envelope_diameter	141.1 Å
Shell Rg shell_rg	41.58 Å
Envelope Rg envelope_rg	36.77 Å
Shape Rg shape_rg	37.27 Å
Total Rg total_rg	37.56 Å
Total atoms total_atoms	8604
Residues n_residues	1063
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	129.6 Å
Rg (real space) rg_real	37.43 Å
Rg uncertainty (real space) rg_real_error	1.17 Å
I(0) (real space) i0_real	2.2050e+08
I(0) uncertainty (real space) i0_real_error	4.2430e+06
Rg (reciprocal space) rg_reciprocal	37.35 Å
I(0) (reciprocal space) i0_reciprocal	220500000.0000
Solution quality estimate total_estimate	0.8745
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.1 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.329
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18790000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PHAGE DISPLAY DERIVED VARIANT HUMAN GROWTH HORMONE
Molecular weight formula_weight	21986.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	8678

FPTIPLSRLADNAWLRADRLNQLAFDTYQEFEEAYIPKEQIHSFWWNPQTSLCPSESIPTPSNKEETQQKSNLELLRISLLLIQSWLEPVQFLRSVFANSLVYGASDSNVYDLLKDLEEGIQTLMGRLEDGSPRTGQIFKQTYSKFDTNSHNDDALLKNYGLLYCFNKDMSKVSTYLRTVQCRSVEGSCGF

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)
Molecular weight formula_weight	27409.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,E,F

FSGSEATAAILSRAPWSLQSVNPGLKTNSSKEPKFTKCRSPERETFSCHWTDEVHHGTKNLGPIQLFYTRRNTQEWTQEWKECPDYVSAGENSCYFNSSFTSIWIPYCIKLTSNGGTVDEKCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRNADIQKGWMVLEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNSGNYGEFSEVLYVTLPQMSQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	74

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7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d1kf9a_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.1 — Long-chain cytokines

Domain ID domain_id	d1kf9b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9c1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9c2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9d_
Class class	a — All alpha proteins
Fold Fold fold	a.26 — 4-helical cytokines
Superfamily Superfamily superfamily	a.26.1 — 4-helical cytokines
Family Family family	a.26.1.1 — Long-chain cytokines

Domain ID domain_id	d1kf9e1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9e2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9f1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

Domain ID domain_id	d1kf9f2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.2 — Fibronectin type III
Family Family family	b.1.2.1 — Fibronectin type III

CATH v4.4 (10 domains)

Domain ID domain_id	1kf9A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1kf9B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9D00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1kf9E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kf9F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	67.289 Å
Unit-cell length b length_b	111.937 Å
Unit-cell length c length_c	95.290 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.3260

fit	/app/data/saxs_computation/kf/1kf9/1kf9.fit
pddf	/app/data/pr_computation/kf/1kf9/1kf9.pr.out
profile	/app/data/saxs_computation/kf/1kf9/1kf9.dat

PHAGE DISPLAY DERIVED VARIANT OF HUMAN GROWTH HORMONE COMPLEXED WITH TWO COPIES OF THE EXTRACELLULAR DOMAIN OF ITS RECEPTOR

1. Protein Identity and Related Structures Protein Identity & Related Structures

EXTRACELLULAR DOMAIN HUMAN GROWTH HORMONE RECEPTOR (1-238)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)