SAXSdb — 1x2t

▼

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

Coagulation factor IX/X-binding protein A chain

OrganismNot specified

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 1–129	Not recorded	Coagulation factor IX/factor X-binding protein B chain × 1 （P23807） CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–129	Not recorded	Coagulation factor IX/factor X-binding protein B chain × 1 （P23807） CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222

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 1X2T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–129（129 aa）	Not recorded	CL CHLORIDE ION × 1 RB RUBIDIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–129（129 aa）	Not recorded	CL CHLORIDE ION × 2 RB RUBIDIUM ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q7LZ71_TRIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 1–129 Author chain C； PDBConstruct 1–129； UniProt 1–129

Coagulation factor IX/factor X-binding protein B chain

OrganismNot specified

UniProt P23807

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 B； UniProt 24–146	Not recorded	Coagulation factor IX/X-binding protein A chain × 1 （Q7LZ71） CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 24–146	Not recorded	Coagulation factor IX/X-binding protein A chain × 1 （Q7LZ71） CA CALCIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 6.5；293 K；PEG 1000, PEG 8000, calcium chloride, MES, pH 6.5, MICROBATCH, temperature 293K	Resolution 1.72 Å R-free 0.222

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 1X2T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BJ3 CRYSTAL STRUCTURE OF COAGULATION FACTOR IX-BINDING PROTEIN (IX-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1998-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa） Fragment：C-TYPE LECTIN CRD DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED BY MIXING WITH EQUAL VOLUME OF 60% AMMONIUM SULPHATE IN 20 MM TRI-HCL BUFFER AT PH 7.8 CONTAINING AND AT ROOM TEMPERATURE	Resolution 2.60 Å R-free 0.271
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN Chain D 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN Chain F 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1IXX CRYSTAL STRUCTURE OF COAGULATION FACTORS IX/X-BINDING PROTEIN (IX/X-BP) FROM VENOM OF HABU SNAKE WITH A HETERODIMER OF C-TYPE LECTIN DOMAINS Deposited 1997-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 24–146（123 aa） Fragment：C-TYPE LECTIN DOMAIN	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；60% SATURATED AMMONIUM SULFATE, 20 MM TRIS-HCL, 3 MM CACL2, PH 7.8	Resolution 2.50 Å R-free 0.221
1J34 Crystal Structure of Mg(II)-and Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein Deposited 2003-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–146（123 aa）	Not recorded	CA CALCIUM ION × 7 MG MAGNESIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；293 K；PEG 6000, Tris-HCl, calcium chloride, magnesium chloride, pH 8, MICROBATCH, temperature 293K	Resolution 1.55 Å R-free 0.212
1J35 Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein Deposited 2003-01-20	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 24–146（123 aa）	Not recorded	CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8；293 K；PEG 6000, Tris-HCl, calcium chloride, pH 8, MICROBATCH, temperature 293K	Resolution 1.80 Å R-free 0.270
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 24–146（123 aa）	Not recorded	CL CHLORIDE ION × 1 RB RUBIDIUM ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280
1X2W Crystal Structure of Apo-Habu IX-bp at pH 4.6 Deposited 2005-04-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 24–146（123 aa）	Not recorded	CL CHLORIDE ION × 2 RB RUBIDIUM ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；AMMONIUM SULPHATE, RUBIDIUM ACETATE, PEGMME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.29 Å R-free 0.280

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IXB_TRIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–123； UniProt 24–146 Author chain D； PDBConstruct 1–123； UniProt 24–146

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1x2t
Deposition date deposition_date	2005-04-26
Structure title title	Crystal Structure of Habu IX-bp at pH 6.5
Keywords keywords	HETERODIMER, DOMAIN SWAPPING, C-TYPE LECTIN-LIKE PROTEIN, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	27.44 Å
Radius of gyration Rg (electron density) rg_electron	26.69 Å
Forward intensity I(0) i0	60669300.00
Molecular weight molecular_weight	58693.0 kDa
Excluded volume excluded_volume	72211 Å³
Envelope volume envelope_volume	87580 Å³
Hydration-shell volume shell_volume	27819 Å³
Envelope diameter envelope_diameter	95.1 Å
Shell Rg shell_rg	33.40 Å
Envelope Rg envelope_rg	26.60 Å
Shape Rg shape_rg	26.69 Å
Total Rg total_rg	27.37 Å
Total atoms total_atoms	4124
Residues n_residues	504
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

▼

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

Maximum dimension Dmax dmax	90.6 Å
Rg (real space) rg_real	27.41 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	6.0670e+07
I(0) uncertainty (real space) i0_real_error	8.6630e+05
Rg (reciprocal space) rg_reciprocal	27.42 Å
I(0) (reciprocal space) i0_reciprocal	60670000.0000
Solution quality estimate total_estimate	0.8928
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.1 Å
Skewness Skewness skewness	0.260
Kurtosis Kurtosis kurtosis	-0.454
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	41470000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Coagulation factor IX/X-binding protein A chain
Molecular weight formula_weight	14655.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4698

DCPSGWSSYEGHCYKPFKLYKTWDDAERFCTEQAKGGHLVSIESAGEADFVAQLVTENIQNTKSYVWIGLRVQGKEKQCSSEWSDGSSVSYENWIEAESKTCLGLEKETGFRKWVNIYCGQQNPFVCEA

Entity 2 Entity 2 polymer

Description description	Coagulation factor IX/factor X-binding protein B chain
Molecular weight formula_weight	14455.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

DCPSDWSSYEGHCYKPFSEPKNWADAENFCTQQHAGGHLVSFQSSEEADFVVKLAFQTFGHSIFWMGLSNVWNQCNWQWSNAAMLRYKAWAEESYCVYFKSTNNKWRSRACRMMAQFVCEFQA

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	4

Entity 4 Entity 4 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	568

▼

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1x2ta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1x2tb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1x2tc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1x2td_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (4 domains)

Domain ID domain_id	1x2tA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1x2tB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1x2tC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1x2tD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

▶

8. Citations (1)

▶

Unit-cell length a length_a	60.710 Å
Unit-cell length b length_b	63.509 Å
Unit-cell length c length_c	66.902 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.720 Å
Low-resolution limit resolution_low	33.260 Å
R factor r_factor	—
R_work r_work	0.1910
R_free r_free	0.2220

fit	/app/data/saxs_computation/x2/1x2t/1x2t.fit
pddf	/app/data/pr_computation/x2/1x2t/1x2t.pr.out
profile	/app/data/saxs_computation/x2/1x2t/1x2t.dat

Crystal Structure of Habu IX-bp at pH 6.5

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

Coagulation factor IX/X-binding protein A chain

State in the Current Structure

Other States of the Same Protein in the Database

Coagulation factor IX/factor X-binding protein B chain

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)