SAXSdb — 6zov

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

Enteropeptidase

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 785–1019	Fragment：CATALYTIC DOMAIN	GBS 4-carbamimidamidobenzoic acid × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；PEG20000	Resolution 2.19 Å R-free 0.250
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 785–1019	Fragment：CATALYTIC DOMAIN	GBS 4-carbamimidamidobenzoic acid × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；PEG20000	Resolution 2.19 Å R-free 0.250
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 785–1019	Fragment：CATALYTIC DOMAIN	GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；PEG20000	Resolution 2.19 Å R-free 0.250
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 785–1019	Fragment：CATALYTIC DOMAIN	GBS 4-carbamimidamidobenzoic acid × 1 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；PEG20000	Resolution 2.19 Å R-free 0.250

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 6ZOV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4DGJ Structure of a human enteropeptidase light chain variant Deposited 2012-01-26	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 785–1019（235 aa）	Mutation：N6D, G21D, G22D, C112S, N142D, K210E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1 M HEPES, 16% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.210
4DGJ Structure of a human enteropeptidase light chain variant Deposited 2012-01-26	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 785–1019（235 aa）	Mutation：N6D, G21D, G22D, C112S, N142D, K210E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1 M HEPES, 16% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.210
4DGJ Structure of a human enteropeptidase light chain variant Deposited 2012-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 785–1019（235 aa）	Mutation：N6D, G21D, G22D, C112S, N142D, K210E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1 M HEPES, 16% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.210
4DGJ Structure of a human enteropeptidase light chain variant Deposited 2012-01-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 785–1019（235 aa）	Mutation：N6D, G21D, G22D, C112S, N142D, K210E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；0.1 M HEPES, 16% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 1.90 Å R-free 0.210
7WQW Structure of Active-EP Deposited 2022-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 524–784（261 aa） Chain B 785–1019（235 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7WQX Structure of Inactive-EP Deposited 2022-01-26	Different construct 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 519–1019（501 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7WQZ Structure of Active-mutEP Deposited 2022-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 524–784（261 aa） Chain B 785–1019（235 aa）	Mutation：H825A, D876A, S971A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7WR7 Structure of Inhibited-EP Deposited 2022-01-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 524–784（261 aa） Chain B 785–1019（235 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 GBS 4-carbamimidamidobenzoic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8H3S Substrate-bound EP, polyA model Deposited 2022-10-09	Different construct Different mutation/modification 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 A 183–784（602 aa） Chain B 785–1019（235 aa）	Mutation：H825A, D876A, S971A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
8H3U Inhibitor-bound EP, polyA model Deposited 2022-10-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 183–784（602 aa） Chain B 785–1019（235 aa）	Mutation：H825A,D876A,S971A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
8ZI4 Cryo-EM structure of wtEP-trypsinogen Deposited 2024-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 182–784（603 aa） Chain D 785–1019（235 aa）	Mutation：H825A/D876A/S971A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8ZIV wtEP-trypsinogen in Tryp-1 Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 182–784（603 aa） Chain D 785–1019（235 aa）	Mutation：H825A/D876A/S971A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
8ZIW enteropeptidase with E574A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 501–784（284 aa） Chain D 785–1019（235 aa）	Mutation：E574A Mutation：H825A/D876A/S971A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
8ZIY trypsinogen-EP-E574A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 182–784（603 aa） Chain D 785–1019（235 aa）	Mutation：E574A Mutation：H825A/D876A/S971A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
8ZIZ enteropeptidase with N619A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 509–784（276 aa） Chain D 785–1019（235 aa）	Mutation：N619A Mutation：H825A/D876A/S971A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
8ZJ4 trypsinogen-EP-N619A Deposited 2024-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 182–784（603 aa） Chain D 785–1019（235 aa）	Mutation：N619A Mutation：H825A/D876A/S971A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.67 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ENTK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 785–1019 Author chain B； PDBConstruct 1–235； UniProt 785–1019 Author chain C； PDBConstruct 1–235； UniProt 785–1019 Author chain D； PDBConstruct 1–235； UniProt 785–1019

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	6zov
Deposition date deposition_date	2020-07-07
Structure title title	ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6
Keywords keywords	PEPTIDASE, HYDROLASE; HYDROLASE
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	31.42 Å
Radius of gyration Rg (electron density) rg_electron	30.61 Å
Forward intensity I(0) i0	187639000.00
Molecular weight molecular_weight	106350.0 kDa
Excluded volume excluded_volume	131750 Å³
Envelope volume envelope_volume	164720 Å³
Hydration-shell volume shell_volume	43689 Å³
Envelope diameter envelope_diameter	94.3 Å
Shell Rg shell_rg	38.61 Å
Envelope Rg envelope_rg	30.36 Å
Shape Rg shape_rg	30.61 Å
Total Rg total_rg	31.29 Å
Total atoms total_atoms	7474
Residues n_residues	938
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	92.8 Å
Rg (real space) rg_real	31.19 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.8760e+08
I(0) uncertainty (real space) i0_real_error	2.6360e+06
Rg (reciprocal space) rg_reciprocal	31.29 Å
I(0) (reciprocal space) i0_reciprocal	187700000.0000
Solution quality estimate total_estimate	0.7143
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.5 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	121200000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.991; Smooth: 0.882

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Enteropeptidase
Molecular weight formula_weight	26379.7 kDa
EC 编号 ec_number	3.4.21.9
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	8003

IVGGSDAKEGAWPWVVGLYYDDRLLCGASLVSSDWLVSAAHCVYGRNLEPSKWTAILGLHMKSNLTSPQTVPRLIDEIVINPHYNRRRKDNDIAMMHLEFKVNYTDYIQPISLPEENQVFPPGRNCSIAGWGTVVYQGTTADILQEADVPLLSNERCQQQMPEYNITENMICAGYEEGGIDSCQGDSGGPLMCQENNRWFLAGVTSFGYECALPNRPGVYARVSRFTEWIQSFLH

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 non-polymer

Description description	4-carbamimidamidobenzoic acid
Molecular weight formula_weight	179.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	451

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6zova_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6zovb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6zovc_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d6zovd_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (4 domains)

Domain ID domain_id	6zovA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6zovB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6zovC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	6zovD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	52.925 Å
Unit-cell length b length_b	147.517 Å
Unit-cell length c length_c	147.518 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	16

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

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	104.310 Å
R factor r_factor	0.2268
R_work r_work	0.2262
R_free r_free	0.2504

fit	/app/data/saxs_computation/zo/6zov/6zov.fit
pddf	/app/data/pr_computation/zo/6zov/6zov.pr.out
profile	/app/data/saxs_computation/zo/6zov/6zov.dat

ENTEROPEPTIDASE IN COMPLEX WITH COMPOUND 6