SAXSdb — 1p5q

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

FK506-binding protein 4

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 145–458 Chain B； UniProt 145–458 Chain C； UniProt 145–458	Fragment：FKBP52 C-TERMINAL DOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；Ammonium Sulfate, Tris, Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.284

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 1P5Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1N1A Crystal Structure of the N-terminal domain of human FKBP52 Deposited 2002-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa） Fragment：the N-terminal fragment (1-140) Chain B 1–139（139 aa） Fragment：the N-terminal fragment (1-140)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；Tris-HCl, Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.40 Å R-free 0.280
1Q1C Crystal structure of N(1-260) of human FKBP52 Deposited 2003-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–259（259 aa） Fragment：RESIDUES (-19)-260	Not recorded	DMS DIMETHYL SULFOXIDE × 5 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG6000, Tris, DMSO, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.90 Å R-free 0.247
1QZ2 Crystal Structure of FKBP52 C-terminal Domain complex with the C-terminal peptide MEEVD of Hsp90 Deposited 2003-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 144–458（315 aa） Fragment：FKBP52 C-terminal Domain Chain B 144–458（315 aa） Fragment：FKBP52 C-terminal Domain Chain C 144–458（315 aa） Fragment：FKBP52 C-terminal Domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；Sodium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.287
4DRJ o-crystal structure of the PPIase domain of FKBP52, Rapamycin and the FRB fragment of mTOR Deposited 2012-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–140（140 aa） Fragment：Fk1 domain, UNP residues 1-140	Not recorded	RAP RAPAMYCIN IMMUNOSUPPRESSANT DRUG × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M BisTris, 1.95M (NH4)2SO4, pH 6.5, vapor diffusion, temperature 293K	Resolution 1.80 Å R-free 0.225
4LAV Crystal Structure Analysis of FKBP52, Crystal Form II Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–260（245 aa） Fragment：UNP residues 16-260	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.80 Å R-free 0.235
4LAV Crystal Structure Analysis of FKBP52, Crystal Form II Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–260（245 aa） Fragment：UNP residues 16-260	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.80 Å R-free 0.235
4LAW Crystal Structure Analysis of FKBP52, Crystal Form III Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–260（245 aa） Fragment：UNP residues 16-260	Not recorded	DMS DIMETHYL SULFOXIDE × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG6000, 0.1 M Tris-HCl, pH 8.0, 5% DMSO, VAPOR DIFFUSION, temperature 293K	Resolution 2.40 Å R-free 0.282
4LAW Crystal Structure Analysis of FKBP52, Crystal Form III Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–260（245 aa） Fragment：UNP residues 16-260	Not recorded	DMS DIMETHYL SULFOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG6000, 0.1 M Tris-HCl, pH 8.0, 5% DMSO, VAPOR DIFFUSION, temperature 293K	Resolution 2.40 Å R-free 0.282
4LAX Crystal Structure Analysis of FKBP52, Complex with FK506 Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–260（245 aa） Fragment：UNP residues 16-260	Not recorded	FK5 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN × 1 DMS DIMETHYL SULFOXIDE × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG6000, 0.1 M Tris-HCl, pH 8.0, 5% DMSO, VAPOR DIFFUSION, temperature 293K	Resolution 2.01 Å R-free 0.219
4LAY Crystal Structure Analysis of FKBP52, Complex with I63 Deposited 2013-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–260（260 aa） Fragment：UNP residues 1-260	Not recorded	I63 {3-[(1R)-3-(3,4-dimethoxyphenyl)-1-({[(2S)-1-(3,3-dimethyl-2-oxopentanoyl)piperidin-2-yl]carbonyl}oxy)propyl]phenoxy}acetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；25% PEG6000, 0.1 M Tris-HCl, pH 8.0, 4% DMSO, VAPOR DIFFUSION, temperature 293K	Resolution 1.70 Å R-free 0.205
4TW8 The Fk1-Fk2 domains of FKBP52 in complex with iFit-FL Deposited 2014-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain A 21–255（235 aa） Fragment：UNP residues 21-255	Not recorded	37M 2-(5-{[({3-[(1R)-1-[({(2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)oxy]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetyl)amino]methyl}-6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；28 % PEG-6000, 2 % DMSO and TrisHCl pH 8.0	Resolution 3.00 Å R-free 0.257
4TW8 The Fk1-Fk2 domains of FKBP52 in complex with iFit-FL Deposited 2014-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: Monomeric	Chain B 21–255（235 aa） Fragment：UNP residues 21-255	Not recorded	37M 2-(5-{[({3-[(1R)-1-[({(2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)oxy]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetyl)amino]methyl}-6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；28 % PEG-6000, 2 % DMSO and TrisHCl pH 8.0	Resolution 3.00 Å R-free 0.257
6RCY CRYSTAL STRUCTURE OF FK1 DOMAIN OF FKBP52 IN COMPLEX WITH A BIO-INSPIRED HYBRID FLUORESCENT LIGAND Deposited 2019-04-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa）	Not recorded	K0T (2~{S})-5-carbamimidamido-2-[[(2~{S})-2-[[(2~{S})-1-[5-(dimethylamino)naphthalen-1-yl]sulfonylpiperidin-2-yl]carbonylamino]-4-phenyl-butanoyl]amino]pentanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.8M potassium phosphate, 0.8M sodium phosphate, 0.1M HEPES, pH 7.5	Resolution 2.30 Å R-free 0.244
8FFV Cryo-EM structure of the GR-Hsp90-FKBP52 complex Deposited 2022-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–459（459 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 DEX DEXAMETHASONE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FKBP4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–336； UniProt 145–458 Author chain B； PDBConstruct 23–336； UniProt 145–458 Author chain C； PDBConstruct 23–336； UniProt 145–458

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1p5q
Deposition date deposition_date	2003-04-28
Structure title title	Crystal Structure of FKBP52 C-terminal Domain
Keywords keywords	ISOMERASE; ISOMERASE
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	36.64 Å
Radius of gyration Rg (electron density) rg_electron	35.82 Å
Forward intensity I(0) i0	160707000.00
Molecular weight molecular_weight	98712.0 kDa
Excluded volume excluded_volume	122710 Å³
Envelope volume envelope_volume	195770 Å³
Hydration-shell volume shell_volume	45853 Å³
Envelope diameter envelope_diameter	111.7 Å
Shell Rg shell_rg	42.31 Å
Envelope Rg envelope_rg	34.42 Å
Shape Rg shape_rg	35.80 Å
Total Rg total_rg	36.41 Å
Total atoms total_atoms	6921
Residues n_residues	843
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	108.0 Å
Rg (real space) rg_real	36.42 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.6070e+08
I(0) uncertainty (real space) i0_real_error	2.5810e+06
Rg (reciprocal space) rg_reciprocal	36.56 Å
I(0) (reciprocal space) i0_reciprocal	160700000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	-0.002
Kurtosis Kurtosis kurtosis	-0.640
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9234000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.979; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.724

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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	FK506-binding protein 4
Molecular weight formula_weight	38435.8 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7448

MGSSHHHHHHSSGLVPRGSHMEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKDKLFDQRELRFEIGEGENLDLPYGLERAIQRMEKGEHSIVYLKPSYAFGSVGKEKFQIPPNAELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLSRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFERLAEEENKAKAEASSGDHPTDTEMKEEQKSNTAGSQSQVETEA

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 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	527

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d1p5qa1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

Domain ID domain_id	d1p5qa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.1 — FKBP immunophilin/proline isomerase

Domain ID domain_id	d1p5qa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1p5qb1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

Domain ID domain_id	d1p5qb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.1 — FKBP immunophilin/proline isomerase

Domain ID domain_id	d1p5qb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1p5qc1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.8 — TPR-like
Family Family family	a.118.8.1 — Tetratricopeptide repeat (TPR)

Domain ID domain_id	d1p5qc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.26 — FKBP-like
Superfamily Superfamily superfamily	d.26.1 — FKBP-like
Family Family family	d.26.1.1 — FKBP immunophilin/proline isomerase

Domain ID domain_id	d1p5qc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1p5qA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1p5qA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	1p5qB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1p5qB02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	1p5qC01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1p5qC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

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8. Citations (1)

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Unit-cell length a length_a	114.274 Å
Unit-cell length b length_b	142.927 Å
Unit-cell length c length_c	170.897 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2160
R_work r_work	0.2120
R_free r_free	0.2840

fit	/app/data/saxs_computation/p5/1p5q/1p5q.fit
pddf	/app/data/pr_computation/p5/1p5q/1p5q.pr.out
profile	/app/data/saxs_computation/p5/1p5q/1p5q.dat

Crystal Structure of FKBP52 C-terminal Domain

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

FK506-binding protein 4

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