3RM2

Human Thrombin in complex with MI003

• PDB DOI: https://doi.org/10.2210/pdb3RM2/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2011-04-20 Released: 2012-04-25 
• Deposition Author(s): Biela, A., Heine, A., Klebe, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.163 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.64 kDa 
• Atom Count: 2,888 
• Modelled Residue Count: 290 
• Deposited Residue Count: 308 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin Light Chain	A [auth L]	36	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin Heavy Chain	B [auth H]	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin variant-2	C [auth I]	13	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S00	E [auth H]	N-(benzylsulfonyl)-3-cyclohexyl-D-alanyl-N-(4-carbamimidoylbenzyl)-L-prolinamide C29 H39 N5 O4 S DJNNZKJZFCRFRX-FTJBHMTQSA-N
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4	F [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth H], H	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	I [auth H], J [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	C [auth I]	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
S00	BindingDB:  3RM2	Ki: min: 0.1, max: 0.12 (nM) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000806 (S00)	E [auth H]	N-(BENZYLSULFONYL)-3-CYCLOHEXYL-D-ALANYL-N-(4-CARBAMIMIDOYLBENZYL)-L-PROLINAMIDE	Peptide-like / Thrombin inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 0.163 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.8	α = 90
b = 71.5	β = 99.9
c = 71.9	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Biela, A., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2016-07-13
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2023-12-06
  Changes: Data collection