SAXSdb — 1tpk

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

TISSUE PLASMINOGEN ACTIVATOR

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 211–298	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 211–298	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 211–298	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 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 1TPK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5H CATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR COMPLEX OF A BIS-BENZAMIDINE Deposited 1998-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 311–562（252 aa） Fragment：LIGHT CHAIN, CATALYTIC DOMAIN Chain C 298–304（7 aa） Fragment：HEAVY CHAIN FRAGMENT, CATALYTIC DOMAIN	Not recorded	BBA 2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.90 Å
1A5H CATALYTIC DOMAIN OF HUMAN TWO-CHAIN TISSUE PLASMINOGEN ACTIVATOR COMPLEX OF A BIS-BENZAMIDINE Deposited 1998-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 311–562（252 aa） Fragment：LIGHT CHAIN, CATALYTIC DOMAIN Chain D 298–304（7 aa） Fragment：HEAVY CHAIN FRAGMENT, CATALYTIC DOMAIN	Not recorded	BBA 2,7-BIS-(4-AMIDINOBENZYLIDENE)-CYCLOHEPTAN-1-ONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.90 Å
1BDA CATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVATOR IN COMPLEX WITH DANSYL-EGR-CMK (DANSYL-GLU-GLY-ARG CHLOROMETHYL KETONE) Deposited 1998-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 298–562（265 aa） Fragment：UNP residues 298-562	Mutation：DELETION MUTANT	2Z0 N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；pH 8.2	Resolution 3.35 Å
1BDA CATALYTIC DOMAIN OF HUMAN SINGLE CHAIN TISSUE PLASMINOGEN ACTIVATOR IN COMPLEX WITH DANSYL-EGR-CMK (DANSYL-GLU-GLY-ARG CHLOROMETHYL KETONE) Deposited 1998-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 298–562（265 aa） Fragment：UNP residues 298-562	Mutation：DELETION MUTANT	2Z0 N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；pH 8.2	Resolution 3.35 Å
1PK2 SOLUTION STRUCTURE OF THE TISSUE-TYPE PLASMINOGEN ACTIVATOR KRINGLE 2 DOMAIN COMPLEXED TO 6-AMINOHEXANOIC ACID AN ANTIFIBRINOLYTIC DRUG Deposited 1991-09-16	Different construct Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 209–298（90 aa）	Not recorded	ACA 6-AMINOHEXANOIC ACID × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1PML KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES Deposited 1994-04-25	Different construct Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 213–298（86 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.38 Å
1PML KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES Deposited 1994-04-25	Different construct Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 213–298（86 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.38 Å
1PML KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES Deposited 1994-04-25	Different construct Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 213–298（86 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.38 Å
1RTF COMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR [(TC)-T-PA] Deposited 1995-11-10	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 311–562（252 aa） Fragment：CATALYTIC DOMAIN	Not recorded	PO4 PHOSPHATE ION × 1 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.265
1TPG F1-G MODULE PAIR RESIDUES 1-91 (C83S) OF TISSUE-TYPE PLASMINOGEN ACTIVATOR (T-PA) (NMR, 298K, PH2.95, REPRESENTATIVE STRUCTURE) Deposited 1995-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–126（91 aa）	Mutation：C83S	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1TPM SOLUTION STRUCTURE OF THE FIBRIN BINDING FINGER DOMAIN OF TISSUE-TYPE PLASMINOGEN ACTIVATOR DETERMINED BY 1H NUCLEAR MAGNETIC RESONANCE Deposited 1993-05-26	Different construct Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–85（50 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1TPN SOLUTION STRUCTURE OF THE FIBRIN BINDING FINGER DOMAIN OF TISSUE-TYPE PLASMINOGEN ACTIVATOR DETERMINED BY 1H NUCLEAR MAGNETIC RESONANCE Deposited 1993-05-26	Different construct Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–85（50 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5BRR Michaelis complex of tPA-S195A:PAI-1 Deposited 2015-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 311–562（252 aa） Fragment：UNP residues 311-562	Mutation：C120A, N173Q, S203A	GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298.15 K；8% PEG 6000, 0.1 M Tris-HCl	Resolution 3.16 Å R-free 0.276
5ZLZ Structure of tPA and PAI-1 Deposited 2018-03-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 311–561（251 aa）	Mutation：C430A, F458E, N483Q, S513A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4-8% PEG 3350, 20 mM bis-Tris-HCl pH 7.0	Resolution 3.58 Å R-free 0.312

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

View Construct and Data Evidence

UniProt name	TPA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–88； UniProt 211–298 Author chain B； PDBConstruct 1–88； UniProt 211–298 Author chain C； PDBConstruct 1–88； UniProt 211–298

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	1tpk
Deposition date deposition_date	1991-09-24
Structure title title	CRYSTAL STRUCTURE OF THE KRINGLE-2 DOMAIN OF TISSUE PLASMINOGEN ACTIVATOR AT 2.4-ANGSTROMS RESOLUTION
Keywords keywords	PLASMINOGEN ACTIVATOR; PLASMINOGEN ACTIVATOR
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	22.42 Å
Radius of gyration Rg (electron density) rg_electron	21.60 Å
Forward intensity I(0) i0	17130300.00
Molecular weight molecular_weight	29041.0 kDa
Excluded volume excluded_volume	35308 Å³
Envelope volume envelope_volume	44186 Å³
Hydration-shell volume shell_volume	18092 Å³
Envelope diameter envelope_diameter	78.8 Å
Shell Rg shell_rg	26.84 Å
Envelope Rg envelope_rg	21.69 Å
Shape Rg shape_rg	21.58 Å
Total Rg total_rg	22.34 Å
Total atoms total_atoms	2028
Residues n_residues	255
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	76.0 Å
Rg (real space) rg_real	22.46 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.7130e+07
I(0) uncertainty (real space) i0_real_error	2.2460e+05
Rg (reciprocal space) rg_reciprocal	22.45 Å
I(0) (reciprocal space) i0_reciprocal	17130000.0000
Solution quality estimate total_estimate	0.8828
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.302
Kurtosis Kurtosis kurtosis	-0.547
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3772000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.992

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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	TISSUE PLASMINOGEN ACTIVATOR
Molecular weight formula_weight	9653.8 kDa
EC 编号 ec_number	3.4.21.31
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2119

GNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCST

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1tpka_
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d1tpkb_
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

Domain ID domain_id	d1tpkc_
Class class	g — Small proteins
Fold Fold fold	g.14 — Kringle-like
Superfamily Superfamily superfamily	g.14.1 — Kringle-like
Family Family family	g.14.1.1 — Kringle modules

CATH v4.4 (3 domains)

Domain ID domain_id	1tpkA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	1tpkB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

Domain ID domain_id	1tpkC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	20 — Plasminogen Kringle 4
Homologous superfamily homologous superfamily	10 — Plasminogen Kringle 4

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8. Citations (1)

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Unit-cell length a length_a	54.800 Å
Unit-cell length b length_b	63.580 Å
Unit-cell length c length_c	46.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	—

fit	/app/data/saxs_computation/tp/1tpk/1tpk.fit
pddf	/app/data/pr_computation/tp/1tpk/1tpk.pr.out
profile	/app/data/saxs_computation/tp/1tpk/1tpk.dat

CRYSTAL STRUCTURE OF THE KRINGLE-2 DOMAIN OF TISSUE PLASMINOGEN ACTIVATOR AT 2.4-ANGSTROMS RESOLUTION

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

TISSUE PLASMINOGEN ACTIVATOR

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