SAXSdb — 1vdn

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

Cyclophilin A

Saccharomyces cerevisiae

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 0–161	Not recorded	(ACE)AAPA(MCM) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；ammonium sulfate, methanol, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.60 Å R-free 0.237

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 1VDN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IST Crystal structure of yeast cyclophilin A, CPR1 Deposited 2001-12-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 0–161（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 6000, EDTA, ethanol, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.216
1IST Crystal structure of yeast cyclophilin A, CPR1 Deposited 2001-12-25	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 0–161（162 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG 6000, EDTA, ethanol, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.216
9CF0 Parasitella parasitica Fanzor (PpFz) State 1 Deposited 2024-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: pentameric	Chain C 1–162（162 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.47 Å
9CF1 Parasitella parasitica Fanzor (PpFz) State 2 Deposited 2024-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: pentameric	Chain C 1–162（162 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.52 Å
9CF2 Parasitella parasitica Fanzor (PpFz) State 3 Deposited 2024-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: heptameric	Chain C 1–162（162 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.15 Å
9CF3 Parasitella parasitica Fanzor (PpFz) State 4 Deposited 2024-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: pentameric	Chain C 1–162（162 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.20 Å

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CYPH_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 0–161

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	1vdn
Deposition date deposition_date	2004-03-24
Structure title title	Crystal Structure Of Yeast Cyclophilin A Complexed With ACE-Ala-Ala-Pro-Ala-7-Amino-4-Methylcoumarin
Keywords keywords	BETA BARREL, ISOMERASE-ISOMERASE INHIBITOR COMPLEX, ROTAMASE; ISOMERASE/ISOMERASE INHIBITOR
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	15.34 Å
Radius of gyration Rg (electron density) rg_electron	14.12 Å
Forward intensity I(0) i0	5919750.00
Molecular weight molecular_weight	17760.0 kDa
Excluded volume excluded_volume	22255 Å³
Envelope volume envelope_volume	23652 Å³
Hydration-shell volume shell_volume	13852 Å³
Envelope diameter envelope_diameter	47.0 Å
Shell Rg shell_rg	20.40 Å
Envelope Rg envelope_rg	14.35 Å
Shape Rg shape_rg	14.10 Å
Total Rg total_rg	15.37 Å
Total atoms total_atoms	1256
Residues n_residues	165
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	47.6 Å
Rg (real space) rg_real	15.19 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	5.9200e+06
I(0) uncertainty (real space) i0_real_error	6.0860e+04
Rg (reciprocal space) rg_reciprocal	15.20 Å
I(0) (reciprocal space) i0_reciprocal	5920000.0000
Solution quality estimate total_estimate	0.8875
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.035
Kurtosis Kurtosis kurtosis	-0.420
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1971000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.979

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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	Cyclophilin A
Molecular weight formula_weight	17411.7 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1444

MSQVYFDVEADGQPIGRVVFKLYNDIVPKTAENFRALCTGEKGFGYAGSPFHRVIPDFMLQGGDFTAGNGTGGKSIYGGKFPDENFKKHHDRPGLLSMANAGPNTNGSQFFITTVPCPWLDGKHVVFGEVVDGYDIVKKVESLGSPSGATKARIVVAKSGEL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	(ACE)AAPA(MCM)
Molecular weight formula_weight	511.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XAAPAX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vdna_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id	1vdnA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

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8. Citations (1)

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Unit-cell length a length_a	31.737 Å
Unit-cell length b length_b	40.009 Å
Unit-cell length c length_c	112.736 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1990
R_free r_free	0.2370

fit	/app/data/saxs_computation/vd/1vdn/1vdn.fit
pddf	/app/data/pr_computation/vd/1vdn/1vdn.pr.out
profile	/app/data/saxs_computation/vd/1vdn/1vdn.dat

Crystal Structure Of Yeast Cyclophilin A Complexed With ACE-Ala-Ala-Pro-Ala-7-Amino-4-Methylcoumarin

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

Cyclophilin A

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

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)