1UMA

ALPHA-THROMBIN (HIRUGEN) COMPLEXED WITH NA-(N,N-DIMETHYLCARBAMOYL)-ALPHA-AZALYSINE

• PDB DOI: https://doi.org/10.2210/pdb1UMA/pdb

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


• Deposited: 1996-03-26 Released: 1996-11-08 
• Deposition Author(s): Nardini, M., Pesce, A., Rizzi, M., Casale, E., Ferraccioli, R., Balliano, G., Milla, P., Ascenzi, P., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.9 kDa 
• Atom Count: 2,658 
• Modelled Residue Count: 299 
• Deposited Residue Count: 305 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-THROMBIN	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
ALPHA-THROMBIN	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 I	C [auth I]	10	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P01050 (Hirudo medicinalis) Explore P01050  Go to UniProtKB:  P01050

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IN2	E [auth H], F [auth H]	N,N-DIMETHYLCARBAMOYL-ALPHA-AZALYSINE C8 H18 N4 O3 NKYYGDMMHLUQBA-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.15	α = 90
b = 71.9	β = 100.49
c = 72.3	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
TNT	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Nardini, M., Pesce, A., Rizzi, M., Casale, E., Ferraccioli, R., Balliano, G., Milla, P., Ascenzi, P., Bolognesi, M.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary