Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 

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

Macromolecule Content

• Total Structure Weight: 35.30 kDa 
• Atom Count: 2738 
• Residue Count: 290 
• Unique protein chains: 3

2UUF

Thrombin-hirugen binary complex at 1.26A resolution

• DOI: 10.2210/pdb2UUF/pdb

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


• Deposited: 2007-03-02 Released: 2007-09-04 
• Deposition Author(s): Ahmed, H.U., Blakeley, M.P., Cianci, M., Cruickshank, D.W.J., Hubbard, J.A., Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.194 
• R-Value Observed: 0.146 

Literature

The Determination of Protonation States in Proteins.

Ahmed, H.U., Blakeley, M.P., Cianci, M., Cruickshank, D.W.J., Hubbard, J.A., Helliwell, J.R.

(2007) Acta Crystallogr D Biol Crystallogr 63: 906

• PubMed: 17642517 
• DOI: 10.1107/S0907444907029976
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The protonation states of aspartic acids and glutamic acids as well as histidine are investigated in four X-ray cases: Ni,Ca concanavalin A at 0.94 A, a thrombin-hirugen binary complex at 1.26 A resolution and two thrombin-hirugen-inhibitor ternary complexes at 1.32 and 1.39 A resolution. The truncation of the Ni,Ca concanavalin A data at various test resolutions between 0.94 and 1.50 A provided a test comparator for the ;unknown' thrombin-hirugen carboxylate bond lengths. The protonation states of aspartic acids and glutamic acids can be determined (on the basis of convincing evidence) even to the modest resolution of 1.20 A as exemplified by our X-ray crystal structure refinements of Ni and Mn concanavalin A and also as indicated in the 1.26 A structure of thrombin, both of which are reported here. The protonation-state indication of an Asp or a Glu is valid provided that the following criteria are met (in order of importance). (i) The acidic residue must have a single occupancy. (ii) Anisotropic refinement at a minimum diffraction resolution of 1.20 A (X-ray data-to-parameter ratio of approximately 3.5:1) is required. (iii) Both of the bond lengths must agree with the expectation (i.e. dictionary values), thus allowing some relaxation of the bond-distance standard uncertainties required to approximately 0.025 A for a '3sigma' determination or approximately 0.04 A for a '2sigma' determination, although some variation of the expected bond-distance values must be allowed according to the microenvironment of the hydrogen of interest. (iv) Although the F(o) - F(c) map peaks are most likely to be unreliable at the resolution range around 1.20 A, if admitted as evidence the peak at the hydrogen position must be greater than or equal to 2.5 sigma and in the correct geometry. (v) The atomic B factors need to be less than 10 A(2) for bond-length differentiation; furthermore, the C=O bond can also be expected to be observed with continuous 2F(o) - F(c) electron density and the C-OH bond with discontinuous electron density provided that the atomic B factors are less than approximately 20 A(2) and the contour level is increased. The final decisive option is to carry out more than one experiment, e.g. multiple X-ray crystallography experiments and ideally neutron crystallography. The complementary technique of neutron protein crystallography has provided evidence of the protonation states of histidine and acidic residues in concanavalin A and also the correct orientations of asparagine and glutamine side chains. Again, the truncation of the neutron data at various test resolutions between 2.5 and 3.0 A, even 3.25 and 3.75 A resolution, examines the limits of the neutron probe. These various studies indicate a widening of the scope of both X-ray and neutron probes in certain circumstances to elucidate the protonation states in proteins.

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Organizational Affiliation: 

School of Chemistry, Brunswick Street, The University of Manchester, Manchester, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HUMAN ALPHA THROMBIN	A	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734 GTEx  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
THROMBIN	B	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734 GTEx  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HIRUDIN I	H	10	Hirudo medicinalis	Mutation(s): 0
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
CA	B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	H	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.194 
• R-Value Observed: 0.146 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.275	α = 90
b = 71.29	β = 99.9
c = 72.037	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing
SHELXL-97	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-03-02 
• Released Date: 2007-09-04 
Deposition Author(s): Ahmed, H.U., Blakeley, M.P., Cianci, M., Cruickshank, D.W.J., Hubbard, J.A., Helliwell, J.R.

Revision History 

• Version 1.0: 2007-09-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Changes: Other
• Version 1.3: 2013-03-13
  Changes: Other
• Version 1.4: 2013-08-07
  Changes: Other
• Version 1.5: 2019-05-22
  Changes: Data collection, Derived calculations, Other, Refinement description