5A2M

Thrombin Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5A2M/pdb

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


• Deposited: 2015-05-20 Released: 2016-06-01 
• Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

Thrombin Inhibition

Ruehmann, E., Heine, A., Klebe, G.

To be published.

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: 35.57 kDa 
• Atom Count: 2,672 
• Modelled Residue Count: 290 
• Deposited Residue Count: 299 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN HEAVY CHAIN	A [auth H]	258	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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P00734-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN VARIANT-2	B [auth I]	12	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P09945 (Hirudo medicinalis) Explore P09945  Go to UniProtKB:  P09945

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN LIGHT CHAIN	C [auth L]	29	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WX5	G [auth H]	(2S)-1-[(2R)-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]-N-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]pyrrolidine-2-carboxamide C26 H35 Cl N6 O5 S LWHZTVPXBHYWTP-PKTZIBPZSA-N
NAG	H	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	D [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth H], F [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.159 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.114	α = 90
b = 71.242	β = 100.13
c = 72.368	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Ruehmann, E., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 2.0: 2019-10-23
  Changes: Atomic model, Data collection, Derived calculations, Other
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.3: 2024-11-20
  Changes: Structure summary