3rm2

Human Thrombin in complex with MI003

Method: X-RAY DIFFRACTION

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

Thrombin Light Chain

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 variant-2 × 1 （P09945） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 PHOSPHATE ION × 1 GLYCEROL × 2 SODIUM ION × 2 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, 2
Chains and sequence ranges	Author chain L； PDBConstruct 1–36； UniProt 328–363 Author chain H； PDBConstruct 1–259； UniProt 364–622

Hirudin variant-2

OrganismNot specified

UniProt P09945

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Thrombin Light Chain × 1 （P00734） Thrombin Heavy Chain × 1 （P00734） 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide × 1 PHOSPHATE ION × 1 GLYCEROL × 2 SODIUM ION × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HIRV2_HIRME
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–13； UniProt 60–72

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	3rm2
Deposition date deposition_date	2011-04-20
Structure title title	Human Thrombin in complex with MI003
Keywords keywords	;Serine Protease, Kringle, Hydrolase, Blood Coagulation, Blood Clotting, Convertion of Fibrinogen to Fibrin, Hirudin, Blood, glycosylation, 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.

3rm2__assembly_1__model_1

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

Download this curve (.dat)

3rm2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rm2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.09 Å
Rg (electron density)	17.89 Å
Total Rg	18.89 Å
Atom count	2409
Residues	289
Excluded volume	42950 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rm2__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 (9)

Entity 1 Entity 1 polymer

Description description	Thrombin Light Chain
Molecular weight formula_weight	4096.5 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
Atom count atom_count	2888

TFGSGEADCGLRPLFEKKSLEDKTERELLESYIDGR

Entity 2 Entity 2 polymer

Description description	Thrombin Heavy Chain
Molecular weight formula_weight	29780.2 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

IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Entity 3 Entity 3 polymer

Description description	Hirudin variant-2
Molecular weight formula_weight	1662.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

NGDFEEIPEEYLQ

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
Molecular weight formula_weight	553.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	390

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3rm2H01
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	3rm2H02
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	69.800 Å
Unit-cell length b length_b	71.500 Å
Unit-cell length c length_c	71.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.90 °
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	1.230 Å
Low-resolution limit resolution_low	20.109 Å
R factor r_factor	0.1415
R_work r_work	0.1404
R_free r_free	0.1629

Human Thrombin in complex with MI003

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

Thrombin Light Chain

State in the Current Structure

Other States of the Same Protein in the Database

Hirudin variant-2

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

3rm2__assembly_1__model_1

3rm2__assembly_1__model_1 | I(q)

3rm2__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 (9)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Human Thrombin in complex with MI003

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

Thrombin Light Chain

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 variant-2

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

3rm2__assembly_1__model_1

3rm2__assembly_1__model_1 | I(q)

3rm2__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 (9)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)