SAXSdb — 6ocx

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

Calcium and integrin-binding protein 1

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 1–191	Not recorded	Peptide inhibitor UNC10245109 × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–191	Not recorded	Peptide inhibitor UNC10245109 × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–191	Not recorded	Peptide inhibitor UNC10245109 × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 Å R-free 0.246
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–191	Not recorded	Peptide inhibitor UNC10245109 × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；294 K；0.1 M HEPES: NaOH, pH 7.5 20 % (w/v) PEG 8000	Resolution 1.90 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 6OCX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DGU HOMOLOGY-BASED MODEL OF CALCIUM-SATURATED CIB (CALCIUM-AND INTEGRIN-BINDING PROTEIN) Deposited 1999-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–191（183 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1DGV HOMOLOGY-BASED MODEL OF APO CIB (CALCIUM-AND INTEGRIN-BINDING PROTEIN) Deposited 1999-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–191（183 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1XO5 Crystal structure of CIB1, an EF-hand, integrin and kinase-binding protein Deposited 2004-10-05	Different construct 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 8–190（183 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；20 mM Bis-Tris-propane (BTP), 300 mM calcium acetate, 18% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.99 Å R-free 0.257
1XO5 Crystal structure of CIB1, an EF-hand, integrin and kinase-binding protein Deposited 2004-10-05	Different construct 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 8–190（183 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；291 K；20 mM Bis-Tris-propane (BTP), 300 mM calcium acetate, 18% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.99 Å R-free 0.257
1Y1A CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN Deposited 2004-11-17	Different construct 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 9–191（183 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
1Y1A CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN Deposited 2004-11-17	Different construct 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 9–191（183 aa）	Not recorded	CA CALCIUM ION × 3 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
1Y1A CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN Deposited 2004-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 9–191（183 aa） Chain B 9–191（183 aa）	Not recorded	CA CALCIUM ION × 12 GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
1Y1A CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN Deposited 2004-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 9–191（183 aa） Chain B 9–191（183 aa）	Not recorded	CA CALCIUM ION × 6 GSH Glutathione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
1Y1A CRYSTAL STRUCTURE OF CALCIUM AND INTEGRIN BINDING PROTEIN Deposited 2004-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 9–191（183 aa）	Not recorded	CA CALCIUM ION × 6 GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；20 MG/ML PROTEIN, 50MM HEPES, 3M FORMATE, 300MM NaCl, 1% DMSO, 0.25MM DTT, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.30 Å R-free 0.251
2L4H The Solution Structure of Calcium Bound CIB1 Deposited 2010-10-06	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium cloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM I/L/V methyl 13C and 1H, [U,2H] CIB1, 50 mM HEPES, 100 mM potassium chloride, 4 mM calcium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L4I The Solution Structure of Magnesium bound CIB1 Deposited 2010-10-06	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	MG MAGNESIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM I/L/V methyl labeled [U, 2H] CIB1, 5 mM MAGNESIUM ION, 100 mM potassium chloride, 10 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LM5 Solution structure of Ca2+-CIB1 in complex with the cytoplasmic domain of the integrin aIIb subunit Deposited 2011-11-22	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–191（191 aa）	Not recorded	CA CALCIUM ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；310 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-10% 13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-2H], I/L/V methyl [1H,13C] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 14 mg/mL pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] CIB1, 5 mM [U-2H] DTT, 2 mM CALCIUM ION, 100 mM sodium chloride, 50 mM HEPES, 0.6 mM aIIb peptide, 5 % C12E5/glycerol (0.96/1), 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6OD0 Structure of human CIB1 in complex with peptide inhibitor UNC10245092 Deposited 2019-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–191（191 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；294 K；137.5 mM calcium acetate, 16 % PEG 3350, 20 mM Bis-Tris propane (pH 6.8)	Resolution 2.15 Å R-free 0.229
6OD0 Structure of human CIB1 in complex with peptide inhibitor UNC10245092 Deposited 2019-03-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–191（191 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.8；294 K；137.5 mM calcium acetate, 16 % PEG 3350, 20 mM Bis-Tris propane (pH 6.8)	Resolution 2.15 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	CIB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–191； UniProt 1–191 Author chain B； PDBConstruct 1–191； UniProt 1–191 Author chain C； PDBConstruct 1–191； UniProt 1–191 Author chain D； PDBConstruct 1–191； UniProt 1–191

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	6ocx
Deposition date deposition_date	2019-03-25
Structure title title	Structure of human CIB1 in complex with peptide inhibitor UNC10245109
Keywords keywords	CIB1, cancer, METAL BINDING PROTEIN; METAL BINDING PROTEIN
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	33.70 Å
Radius of gyration Rg (electron density) rg_electron	33.18 Å
Forward intensity I(0) i0	90601500.00
Molecular weight molecular_weight	76346.0 kDa
Excluded volume excluded_volume	95791 Å³
Envelope volume envelope_volume	132080 Å³
Hydration-shell volume shell_volume	33665 Å³
Envelope diameter envelope_diameter	111.0 Å
Shell Rg shell_rg	39.22 Å
Envelope Rg envelope_rg	32.71 Å
Shape Rg shape_rg	33.15 Å
Total Rg total_rg	33.79 Å
Total atoms total_atoms	5373
Residues n_residues	696
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	108.7 Å
Rg (real space) rg_real	33.63 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	9.0600e+07
I(0) uncertainty (real space) i0_real_error	1.4660e+06
Rg (reciprocal space) rg_reciprocal	33.67 Å
I(0) (reciprocal space) i0_reciprocal	90600000.0000
Solution quality estimate total_estimate	0.8196
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.164
Kurtosis Kurtosis kurtosis	-0.495
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13620000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Calcium and integrin-binding protein 1
Molecular weight formula_weight	21727.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5802

MGGSGSRLSKELLAEYQDLTFLTKQEILLAHRRFCELLPQEQRSVESSLRAQVPFEQILSLPELKANPFKERICRVFSTSPAKDSLSFEDFLDLLSVFSDTATPDIKSHYAFRIFDFDDDGTLNREDLSRLVNCLTGEGEDTRLSASEMKQLIDNILEESDIDRDGTINLSEFQHVISRSPDFASSFKIVL

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	Peptide inhibitor UNC10245109
Molecular weight formula_weight	1724.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,H,J,L

DGGSFWYRAMKALYG

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	377

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6ocxA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	6ocxB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	6ocxC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	6ocxD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	75.866 Å
Unit-cell length b length_b	33.035 Å
Unit-cell length c length_c	162.402 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.85 °
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	1.900 Å
Low-resolution limit resolution_low	27.640 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2460

fit	/app/data/saxs_computation/oc/6ocx/6ocx.fit
pddf	/app/data/pr_computation/oc/6ocx/6ocx.pr.out
profile	/app/data/saxs_computation/oc/6ocx/6ocx.dat

Structure of human CIB1 in complex with peptide inhibitor UNC10245109

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

Calcium and integrin-binding protein 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)