SAXSdb — 7v1n

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

Toxin B

Clostridioides difficile

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 1–2367	Not recorded	Isoform Beta of Tissue factor pathway inhibitor × 1 （P10646）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TCDB2_CLODI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–2367； UniProt 1–2367

Isoform Beta of Tissue factor pathway inhibitor

Homo sapiens

UniProt P10646

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 K； UniProt 1–251	Not recorded	Toxin B × 1 （Q9EXR0）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.20 Å

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 7V1N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ADZ THE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR, NMR, 30 STRUCTURES Deposited 1997-02-19	Different construct Different mutation/modification 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 107–182（76 aa） Fragment：FACTOR XA-BINDING DOMAIN (DOMAIN II)	Mutation：N-TERMINAL INS(DYKDDDDKL)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4.5；310 K；Pressure 1	Resolution not provided
1IRH The Solution Structure of The Third Kunitz Domain of Tissue Factor Pathway Inhibitor Deposited 2001-10-02	Different construct 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 210–270（61 aa） Fragment：the third kunitz domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1mM the third kunitz domain of tissue factor pathway inhibitor U-15N; 20mM Na-phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM the third kunitz domain of tissue factor pathway inhibitor U-15N, 13C; 20mM Na-phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
1TFX COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN Deposited 1997-01-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 121–178（58 aa） Fragment：FACTOR XA-BINDING DOMAIN, DOMAIN II	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å
1TFX COMPLEX OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR WITH PORCINE TRYPSIN Deposited 1997-01-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 121–178（58 aa） Fragment：FACTOR XA-BINDING DOMAIN, DOMAIN II	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å
4DTG Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model Deposited 2012-02-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 119–178（60 aa） Fragment：Kunitz-type protease inhibitor domain 2 (UNP residues 119-178)	Not recorded	GOL GLYCEROL × 10 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；295 K；0.05 M CALCIUM CHLORIDE, 0.1 M MES, pH 6.0, 45% V/V PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.80 Å R-free 0.236
5NMV Crystal structure of 2F22 Fab fragment against TFPI1 Deposited 2017-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 29–107（79 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20 % PEG 3350 200 mM Potassium formate	Resolution 1.65 Å R-free 0.202
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
6BX8 Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) Deposited 2017-12-18	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 50–107（58 aa）	Mutation：K64R, M66C, I83C	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27)	Resolution 1.98 Å R-free 0.221
9P0X Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted) Deposited 2025-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain K 40–107（68 aa）	Not recorded	MG MAGNESIUM ION × 4 CA CALCIUM ION × 12 BGC beta-D-glucopyranose × 1 FUC alpha-L-fucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	TFPI1_HUMAN
Isoform	P10646-2
PDB entities	2
Chains and sequence ranges	Author chain K； PDBConstruct 1–251； UniProt 1–251

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	7v1n
Deposition date deposition_date	2021-08-05
Structure title title	Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI
Keywords keywords	TcdB4, TFPI, receptor, complex, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	62.32 Å
Radius of gyration Rg (electron density) rg_electron	63.48 Å
Forward intensity I(0) i0	1038420000.00
Molecular weight molecular_weight	271040.0 kDa
Excluded volume excluded_volume	339570 Å³
Envelope volume envelope_volume	561390 Å³
Hydration-shell volume shell_volume	82424 Å³
Envelope diameter envelope_diameter	244.7 Å
Shell Rg shell_rg	53.42 Å
Envelope Rg envelope_rg	64.95 Å
Shape Rg shape_rg	63.58 Å
Total Rg total_rg	62.81 Å
Total atoms total_atoms	19150
Residues n_residues	2403
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	214.8 Å
Rg (real space) rg_real	63.15 Å
Rg uncertainty (real space) rg_real_error	2.25 Å
I(0) (real space) i0_real	1.0370e+09
I(0) uncertainty (real space) i0_real_error	2.4550e+07
Rg (reciprocal space) rg_reciprocal	61.36 Å
I(0) (reciprocal space) i0_reciprocal	1035000000.0000
Solution quality estimate total_estimate	0.8139
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	60.1 Å
Skewness Skewness skewness	0.679
Kurtosis Kurtosis kurtosis	0.019
Angular range angular_range	— – 0.1250 Å⁻¹
Current regularization parameter α current_alpha	0.0056
Highest regularization parameter α highest_alpha	51460000.0000
Real-space data points n_real_points	26
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.424

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Toxin B
Molecular weight formula_weight	270454.0 kDa
EC 编号 ec_number	3.4.22.-
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	19156

MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDTYIDTYKKSGRNKALKKFKEYLVTEILELKNSNLTPVEKNLHFIWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTIIESASNDTLESFRENLNDPEFNHTAFFRKRMQIIYDKQQNFINYYKAQKEENPDLIIDDIVKTYLSNEYSKDIDELNAYIEESLNKVTENSGNDVRNFEEFKTGEVFNLYEQELVERWNLAGASDILRVAILKNIGGVYLDVDMLPGIHPDLFKDINKPDSVKTAVDWEEMQLEAIMKYKEYIPEYTSKHFDTLDEEVQSSFESVLASKSDKSEIFLPLGDIEVSPLEVKVAFAKGSIINQALISAKDSYCSDLLIKQIQNRYKILNDTLGPIISQGNDFNTTMNNFGESLGAIANEENISFIAKIGSYLRVGFYPEANTTITLSGPTIYAGAYKDLLTFKEMSIDTSILSSELRNFEFPKVNISQATEQEKNSLWQFNEERAKIQFEEYKKNYFEGALGEDDNLDFSQNTVTDKEYLLEKISSSTKSSERGYVHYIVQLQGDKISYEAACNLFAKNPYDSILFQKNIEDSEVAYYYNPTDSEIQEIDKYRIPDRISDRPKIKLTLIGHGKAEFNTDIFAGLDVDSLSSEIETIIDLAKADISPKSIEINLLGCNMFSYSVNVEETYPGKLLLRVKDKVSELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKIIVKSKNLPELSTLLQEIRNNSNSSDIELEEKVMLAECEINVISNIETQVVEERIEEAKSLTSDSINYIKNEFKLIESISDALYDLKQQNELEESHFISFEDISKTDEGFSIRFIDKETGESIFVETEKAIFSEYANHITEEISKLKDTIFDTVNGKLVKKVTLDATHEVNTLNAAFFIQSLIGYNSSKESLSNLSVAMKVQVYAQLFSTGLNTITDAAKVVELVSTALDETIDLLPTLSEGLPVIATIIDGVSLGASIKELSETSDPLLRQEIEAKIGIMAVNLTAATTAIITSSLGIASGFSILLVPLAGISAGIPSLVNNELILRAEAKNVVDYFGHISLAESEGAFTLLDDKIMMPQDDLVISEIDFNNNSITLGKCEIWRMEGGSGHTVTDDIDHFFSAPSTTYREPYLSIYDVLDVKKEELDLSKDLMVLPNAPDRIFGWERGWTPGLRSLENDGTKLLDRIRDHYEGQFYWRFFAFIADSVITKLKPRYEDTNIRISLDSNTRSFIVPVITTEYIREKLSYSFYGSGGTYALSLSQYNMNINIELNENDTWVIDVDNVVRDVTIESDKIKKGDLIENILSKLSIEDNKIILDNHEINFSGTLNGGNGFVSLTFSILEGINAVIEVDLLSKSYKVLISGELKTLMANSNSVQQKIDYIGLNSELQKNIPYSFMDDEGKENGFINCFTKEGLFVSELSDVVLIIKVYMDNSKPPFGYYSNDLKDVKVITKDDVIILTGYYLKDDIKISLSFTIQDKNTIKLNGVYLDENGVAEILKFMNKKGSTNTSDSLMSFLESMNIKSIFIKSLKSNAKLILDTNFIISGTTSIGQFEFICDKDNNIQPYFIKFNTLETKYTLYVGNRQNMIVEPNYNLDDSGDISSTVINFSQKYLYGIDSCVNKVIISPNIYTDEINITPVHEANNTYPEVIVLDTNYISEKINININDLSIRYVWSNDGSDFILMSTDEENKVSQVKIRFTNVFKGNTISDKISFNFSDKQDISINKIISTFTPSYYVEGLLNYDLGLISLYNEKFYINNLGMMVSGLVYINDSLYYFKPPIKNLITGFTTIGDDKYYFNPDNGGAASVGETIIDGKNYYFSQNGVLQTGVFSTEDGFKYFAPADTLDENLEGEAIDFTGKLIIDENVYYFGDNYRAAIEWQTLDDEVYYFSTDTGRAFKGLNQIGDDKFYFNSDGIMQKGFVNINDKTFYFDDSGVMKSGYTEIDGKYFYFAENGEMQIGVFNTADGFKYFAHHDEDLGNEEGEALSYSGILNFNNKIYYFDDSFTAVVGWKDLEDGSKYYFDENTAEASIGISIINDGKYYFNDSGIMQIGFVTINNEVFYFSDSGIVESGMQNIDDNYFYISENGLVQIGVFDTSDGYKYFAPANTVNDNIYGQAVEYSGLVRVNEDVYSFGESYTIETGWIYDSENESDKYYFDPETKKAYKGINVIDDIKYYFDENGIMRTGLITFEDNHYYFNEDGEMQYGYLNIEDKMFYFSEDGIMQIGVFNTPDGFKYFAHQNTLDENFEGESINYTGWLDLDEKRYYFTDEYIAATGSVIIDGEEYYFDPDTAQLVISEHHHHHHHH

来源 Source

来源生物 organism	Clostridioides difficile
通用名 common_name	Peptoclostridium difficile
NCBI Class编号 ncbi_taxonomy_id	1496
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Isoform Beta of Tissue factor pathway inhibitor
Molecular weight formula_weight	28681.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MIYTMKKVHALWASVCLLLNLAPAPLNADSEEDEEHTIITDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEECKKMCTRDNANRIIKTTLQQEKPDFCFLEEDPGICRGYITRYFYNNQTKQCERFKYGGCLGNMNNFETLEECKNICEDGPNGFQVDNYGTQLNAVNNSLTPQSTKVPSLFVTKEGTNDGWKNAAHIYQVFLNAFCIHASMFFLGLDSISCLC

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	Homo sapiens

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7v1nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11050 — MARTX cysteine protease (CPD) domain

Domain ID domain_id	7v1nA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

Domain ID domain_id	7v1nA03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	227825

fit	/app/data/saxs_computation/v1/7v1n/7v1n.fit
pddf	/app/data/pr_computation/v1/7v1n/7v1n.pr.out
profile	/app/data/saxs_computation/v1/7v1n/7v1n.dat

Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI

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

Toxin B

State in the Current Structure

Other States of the Same Protein in the Database

Isoform Beta of Tissue factor pathway inhibitor

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)