SAXSdb — 1vbt

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

CYCLOPHILIN A

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–164	Not recorded	SULFUR-SUBSTITUTED TETRAPEPTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；pH 8.2	Resolution 2.30 Å R-free 0.246
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–164	Not recorded	SULFUR-SUBSTITUTED TETRAPEPTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.2；pH 8.2	Resolution 2.30 Å R-free 0.246

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 1VBT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CWA X-RAY STRUCTURE OF A MONOMERIC CYCLOPHILIN A-CYCLOSPORIN A CRYSTAL COMPLEX AT 2.1 ANGSTROMS RESOLUTION Deposited 1995-09-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1CWB THE X-RAY STRUCTURE OF (MEBM2T)1-CYCLOSPORIN COMPLEXED WITH CYCLOPHILIN A PROVIDES AN EXPLANATION FOR ITS ANOMALOUSLY HIGH IMMUNOSUPPRESSIVE ACTIVITY Deposited 1995-09-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1CWC IMPROVED BINDING AFFINITY FOR CYCLOPHILIN A BY A CYCLOSPORIN DERIVATIVE SINGLY MODIFIED AT ITS EFFECTOR DOMAIN Deposited 1995-09-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.86 Å
1CWJ HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL 3-S-METHYL-SARCOSINE CYCLOSPORIN Deposited 1998-05-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PH 8.0	Resolution 1.80 Å
1CWK HUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7-DIHYDRO)MEBMT 2-VAL 3-D-(2-S-METHYL)SARCOSINE CYCLOSPORIN Deposited 1998-05-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PH 8.0	Resolution 1.80 Å
1CWL HUMAN CYCLOPHILIN A COMPLEXED WITH 4 4-HYDROXY-MELEU CYCLOSPORIN Deposited 1998-05-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PH 8.0	Resolution 1.80 Å
1MIK THE ROLE OF WATER MOLECULES IN THE STRUCTURE-BASED DESIGN OF (5-HYDROXYNORVALINE)-2-CYCLOSPORIN: SYNTHESIS, BIOLOGICAL ACTIVITY, AND CRYSTALLOGRAPHIC ANALYSIS WITH CYCLOPHILIN A Deposited 1995-09-20	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.76 Å
1RMH RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL Deposited 1995-07-31	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 A 1–164（164 aa） Chain B 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1VBS STRUCTURE OF CYCLOPHILIN COMPLEXED WITH (D)ALA CONTAINING TETRAPEPTIDE Deposited 1998-06-16	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；pH 8.2	Resolution 2.00 Å R-free 0.247
2CYH CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE ALA-PRO Deposited 1996-02-27	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 1–164（164 aa）	Not recorded	ALA ALANINE × 1 PRO PROLINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.64 Å
3CYH CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE SER-PRO Deposited 1996-02-27	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 1–164（164 aa）	Not recorded	SER SERINE × 1 PRO PROLINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
3CYS DETERMINATION OF THE NMR SOLUTION STRUCTURE OF THE CYCLOPHILIN A-CYCLOSPORIN A COMPLEX Deposited 1994-02-28	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–164（164 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
4CYH CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE HIS-PRO Deposited 1996-02-27	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 1–164（164 aa）	Not recorded	HIS HISTIDINE × 1 PRO PROLINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
5CYH CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO Deposited 1996-02-27	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 1–164（164 aa）	Not recorded	GLY GLYCINE × 1 PRO PROLINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å

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

View Construct and Data Evidence

UniProt name	CYPH_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–165； UniProt 1–164 Author chain B； PDBConstruct 2–165； UniProt 1–164

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	1vbt
Deposition date deposition_date	1998-06-16
Structure title title	Structure of cyclophilin complexed with sulfur-substituted tetrapeptide AAPF
Keywords keywords	CYCLOPHILIN A, PEPTIDYL-PROLYL ISOMERASE, COMPETITIVE INHIBITOR, ISOMERASE-ISOMERASE SUBSTRATE COMPLEX; ISOMERASE/ISOMERASE SUBSTRATE
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	23.28 Å
Radius of gyration Rg (electron density) rg_electron	22.75 Å
Forward intensity I(0) i0	23587800.00
Molecular weight molecular_weight	36850.0 kDa
Excluded volume excluded_volume	45953 Å³
Envelope volume envelope_volume	53085 Å³
Hydration-shell volume shell_volume	20251 Å³
Envelope diameter envelope_diameter	73.5 Å
Shell Rg shell_rg	28.60 Å
Envelope Rg envelope_rg	22.69 Å
Shape Rg shape_rg	22.74 Å
Total Rg total_rg	23.51 Å
Total atoms total_atoms	3170
Residues n_residues	334
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	74.0 Å
Rg (real space) rg_real	23.38 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	2.3590e+07
I(0) uncertainty (real space) i0_real_error	3.0070e+05
Rg (reciprocal space) rg_reciprocal	23.36 Å
I(0) (reciprocal space) i0_reciprocal	23590000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9555000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.920

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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	18036.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3374

MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

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	SULFUR-SUBSTITUTED TETRAPEPTIDE
Molecular weight formula_weight	540.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

AAPFX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vbta_
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)

Domain ID domain_id	d1vbtb_
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 (2 domains)

Domain ID domain_id	1vbtA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	1vbtB00
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	37.700 Å
Unit-cell length b length_b	109.100 Å
Unit-cell length c length_c	118.200 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2460

fit	/app/data/saxs_computation/vb/1vbt/1vbt.fit
pddf	/app/data/pr_computation/vb/1vbt/1vbt.pr.out
profile	/app/data/saxs_computation/vb/1vbt/1vbt.dat

Structure of cyclophilin complexed with sulfur-substituted tetrapeptide AAPF

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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)