SAXSdb — 1egt

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

THROMBOMODULIN

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 427–444	Mutation：DEL(ILE 420)	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1EGT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ADX FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, 14 STRUCTURES Deposited 1997-02-18	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–444（40 aa） Fragment：FIFTH EGF-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K	Resolution not provided
1DQB NMR STRUCTURE OF THROMBOMODULIN EGF(4-5) Deposited 2000-01-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 344–426（83 aa） Fragment：THE FOURTH AND FIFTH EGF-LIKE DOMAINS	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	SOLUTION NMR NMR measurement conditions pH 6.5；310 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition 1mM TM45 U-15N; 90% H2O, 10% D2O, pH 6.5 \| 90% H2O/10% D2O NMR sample composition 1mM TM45; 100% D2O \| 100% D2O	Resolution not provided
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20	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: tetrameric	Chain I 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6	Mutation：YES	FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE	Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric	Chain J 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6	Mutation：YES	FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE	Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric	Chain K 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6	Mutation：YES	FMT FORMIC ACID × 1 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE	Resolution 2.30 Å R-free 0.241
1DX5 Crystal structure of the thrombin-thrombomodulin complex Deposited 1999-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric	Chain L 363–480（118 aa） Fragment：EGF-LIKE DOMAINS 4 - 6	Mutation：YES	FMT FORMIC ACID × 2 CA CALCIUM ION × 1 NA SODIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.1 M NA ACETATE (PH 4.6), 1.8 M NA FORMATE, 0.002 M CA CHLORIDE	Resolution 2.30 Å R-free 0.241
1FGD EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 11 STRUCTURES) Deposited 1995-11-28	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 427–444（18 aa） Fragment：C-TERMINAL SUBDOMAIN, RESIDUES 409 - 426, OF 5TH EPIDERMAL GROWTH FACTOR (EGF)	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1FGE EPIDERMAL GROWTH FACTOR (EGF) SUBDOMAIN OF HUMAN THROMBOMODULIN (NMR, 14 STRUCTURES) Deposited 1995-11-28	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 425–444（20 aa） Fragment：C-TERMINAL SUBDOMAIN, RESIDUES 407 - 426, OF 5TH EPIDERMAL GROWTH FACTOR (EGF)	Mutation：C409A	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1HLT THE STRUCTURE OF A NONADECAPEPTIDE OF THE FIFTH EGF DOMAIN OF THROMBOMODULIN COMPLEXED WITH THROMBIN Deposited 1994-08-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 426–444（19 aa）	Not recorded	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1TMR THE STRUCTURE OF A 19 RESIDUE FRAGMENT FROM THE C-LOOP OF THE FOURTH EPIDERMAL GROWTH FACTOR-LIKE DOMAIN OF THROMBOMODULIN Deposited 1994-05-20	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 389–407（19 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ZAQ FOURTH EGF-LIKE DOMAIN OF THROMBOMODULIN, NMR, 12 STRUCTURES Deposited 1995-09-09	Different construct Different mutation/modification	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–407（44 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2ADX FIFTH EGF-LIKE DOMAIN OF THROMBOMODULIN (TMEGF5), NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-02-18	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 405–444（40 aa） Fragment：FIFTH EGF-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K	Resolution not provided
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06	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 X 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483	Mutation：M388L,R456G,H457Q	SO4 SULFATE ION × 7 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.259
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483	Mutation：M388L,R456G,H457Q	SO4 SULFATE ION × 5 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.259
3GIS Crystal Structure of Na-free Thrombin in Complex with Thrombomodulin Deposited 2009-03-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Z 363–483（121 aa） Fragment：Thrombomodulin EGF domains 4-5-6, UNP residues 363-483	Mutation：M388L,R456G,H457Q	SO4 SULFATE ION × 3 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；294 K；0.2M LiSO4, 22% PEG3350, pH7.0, vapor diffusion, temperature 294K, VAPOR DIFFUSION	Resolution 2.40 Å R-free 0.259
5TO3 Crystal structure of thrombin mutant W215A/E217A fused to EGF456 of thrombomodulin via a 31-residue linker and bound to PPACK Deposited 2016-10-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 363–483（121 aa）	Mutation：W215A, E217A	0G6 D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide × 1 K POTASSIUM ION × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；100 mM HEPES and 20% PEG 8000	Resolution 2.34 Å R-free 0.255
7T4R CryoEM structure of the HCMV Pentamer gH/gL/UL128/UL130/UL131A in complex with THBD and neutralizing fabs MSL-109 and 13H11 Deposited 2021-12-10	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 × 19 PDB declaration: nonadecameric	Chain A 1–516（516 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.5s before plunging	Resolution 3.30 Å

12 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRBM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–17； UniProt 427–444

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	1egt
Deposition date deposition_date	1994-10-12
Structure title title	THROMBIN-BOUND STRUCTURE OF AN EGF SUBDOMAIN FROM HUMAN THROMBOMODULIN DETERMINED BY TRANSFERRED NUCLEAR OVERHAUSER EFFECTS
Keywords keywords	EGF, EPIDERMAL GROWTH FACTOR, BLOOD COAGULATION INHIBITOR; BLOOD COAGULATION INHIBITOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	8.03 Å
Radius of gyration Rg (electron density) rg_electron	7.36 Å
Forward intensity I(0) i0	756614.00
Molecular weight molecular_weight	5697.0 kDa
Excluded volume excluded_volume	6839 Å³
Envelope volume envelope_volume	3382 Å³
Hydration-shell volume shell_volume	4128 Å³
Envelope diameter envelope_diameter	27.4 Å
Shell Rg shell_rg	12.23 Å
Envelope Rg envelope_rg	8.41 Å
Shape Rg shape_rg	7.38 Å
Total Rg total_rg	8.29 Å
Total atoms total_atoms	717
Residues n_residues	51
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	29.2 Å
Rg (real space) rg_real	8.06 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	7.5660e+05
I(0) uncertainty (real space) i0_real_error	7.4820e+03
Rg (reciprocal space) rg_reciprocal	8.06 Å
I(0) (reciprocal space) i0_reciprocal	756600.0000
Solution quality estimate total_estimate	0.6857
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	8.5 Å
Skewness Skewness skewness	0.351
Kurtosis Kurtosis kurtosis	-0.332
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3480.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.640; Smooth: 0.736

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1egta_
Class class	j — Peptides
Fold Fold fold	j.45 — Thrombomodulin EGF domain fragment (residues 409-426)
Superfamily Superfamily superfamily	j.45.1 — Thrombomodulin EGF domain fragment (residues 409-426)
Family Family family	j.45.1.1 — Thrombomodulin EGF domain fragment (residues 409-426)

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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	1

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

Description description	THROMBOMODULIN
Molecular weight formula_weight	1905.0 kDa
Mutation mutation	DEL(ILE 420)
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	717

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

THROMBIN-BOUND STRUCTURE OF AN EGF SUBDOMAIN FROM HUMAN THROMBOMODULIN DETERMINED BY TRANSFERRED NUCLEAR OVERHAUSER EFFECTS

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

THROMBOMODULIN

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/eg/1egt/1egt.fit
pddf	/app/data/pr_computation/eg/1egt/1egt.pr.out
profile	/app/data/saxs_computation/eg/1egt/1egt.dat