SAXSdb — 1h8i

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

THROMBIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HIRUDIN I × 1 （P01050） N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THRB_HUMAN
Isoform	—
PDB entities	1, 3
Chains and sequence ranges	Author chain H； PDBConstruct 1–148； UniProt 364–511 Author chain H； PDBConstruct 149–253； UniProt 518–622 Author chain L； PDBConstruct 1–27； UniProt 334–360

HIRUDIN I

OrganismNot specified

UniProt P01050

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	THROMBIN × 1 （P00734） THROMBIN × 1 （P00734） N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ITH1_HIRME
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–10； UniProt 55–64

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	1h8i
Deposition date deposition_date	2001-02-08
Structure title title	X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.
Keywords keywords	SERINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1h8i__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1h8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h8i__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	19.11 Å
Rg (electron density)	17.90 Å
Total Rg	18.89 Å
Atom count	2412
Residues	289
Excluded volume	42964 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h8i__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	THROMBIN
Molecular weight formula_weight	29208.6 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	2777

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 2 Entity 2 polymer

Description description	HIRUDIN I
Molecular weight formula_weight	1363.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

DFEEIPEEYL

Entity 3 Entity 3 polymer

Description description	THROMBIN
Molecular weight formula_weight	3188.6 kDa
EC 编号 ec_number	3.4.21.5
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ADCGLRPLFEKKSLEDKTERELLESYI

Entity 4 Entity 4 non-polymer

Description description	N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide
Molecular weight formula_weight	637.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	365

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1h8i.1
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 (2 domains)

Domain ID domain_id	1h8iH01
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	1h8iH02
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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Unit-cell length a length_a	70.393 Å
Unit-cell length b length_b	71.301 Å
Unit-cell length c length_c	72.416 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2350

X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.

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

THROMBIN

State in the Current Structure

Other States of the Same Protein in the Database

HIRUDIN I

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1h8i__assembly_1__model_1

1h8i__assembly_1__model_1 | I(q)

1h8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)

X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor.

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

THROMBIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIRUDIN I

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1h8i__assembly_1__model_1

1h8i__assembly_1__model_1 | I(q)

1h8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (2)