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- PDB-1ath: THE INTACT AND CLEAVED HUMAN ANTITHROMBIN III COMPLEX AS A MODEL ... -

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Basic information

Entry
Database: PDB / ID: 1ath
TitleTHE INTACT AND CLEAVED HUMAN ANTITHROMBIN III COMPLEX AS A MODEL FOR SERPIN-PROTEINASE INTERACTIONS
ComponentsANTITHROMBIN III
KeywordsHUMAN ANTITHROMBIN-III
Function / homology
Function and homology information


regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding ...regulation of blood coagulation / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / serine-type endopeptidase inhibitor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / heparin binding / collagen-containing extracellular matrix / protease binding / blood microparticle / endoplasmic reticulum lumen / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Antithrombin-III, serpin domain / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsSchreuder, H.A. / Hol, W.G.J.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: The intact and cleaved human antithrombin III complex as a model for serpin-proteinase interactions.
Authors: Schreuder, H.A. / de Boer, B. / Dijkema, R. / Mulders, J. / Theunissen, H.J. / Grootenhuis, P.D. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Analysis of Human Antithrombin III
Authors: Schreuder, H.A. / De Boer, B. / Pronk, S. / Hol, W.G.J. / Dijkema, R. / Mulders, J. / Theunissen, H.J.M.
History
DepositionDec 14, 1993Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 700SHEET SHEETS A AND A2 ARE PARTIALLY OPENED (SEE NATURE STRUCTURAL BIOLOGY PAPER). ONLY TWO RESIDUES ...SHEET SHEETS A AND A2 ARE PARTIALLY OPENED (SEE NATURE STRUCTURAL BIOLOGY PAPER). ONLY TWO RESIDUES OF STRAND 4A (THE REACTIVE SITE LOOP) ARE INSERTED IN SHEETS A AND A2. STRANDS 3A AND 5A MAKE DIRECT PARALLEL CONTACTS AT THE OTHER SIDE OF THE SHEET. THESE REGIONS AND THE REGISTRATION ARE GIVEN BELOW: STRAND 3 LEU 213 ASN 217 0 STRAND 5 PHE 368 VAL 375 +1 LEU 215 O - PHE 368 N. SHEETS C AND C2: PART OF THESE SHEETS IS STRONGLY TWISTED. EACH OF THESE SHEETS ALSO CONTAINS A STRAND (COMPRISING RESIDUES 400 - 403 FOR SHEET C, 387 - 390 FOR SHEET C2) THAT BELONGS TO A DIFFERENT MOLECULE. THESE STRANDS ARE, IN FACT, THE REACTIVE SITE LOOP IN THE 'ACTIVE CONFORMATION'. BECAUSE OF THE PDB REPRESENTATION OF SHEETS IT IS NOT POSSIBLE TO INCLUDE THESE STRANDS ON SHEET RECORDS BELOW. THE HYDROGEN BONDING LADDERS OF SHEETS B (AND B2) AND C (AND C2) OVERLAP IN ONE CORNER NEAR RESIDUES 812 - 813. THE ORIENTATION OF THE SHEETS IS, HOWEVER, SUFFICIENTLY DIFFERENT TO CALL THEM SEPARATE SHEETS. THE ORIENTATION OF RESIDUES 812 - 813 MOST CLOSELY MATCHES SHEET B (AND B2). THEY HAVE BEEN NAMED STRAND 0 IN ORDER TO REMAIN CONSISTENT WITH EXISTING NOMENCLATURE [SEE E.G. J. MOL. BIOL. 232 (1993), 223 - 241].

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTITHROMBIN III
B: ANTITHROMBIN III


Theoretical massNumber of molelcules
Total (without water)98,2022
Polymers98,2022
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.950, 101.170, 69.519
Angle α, β, γ (deg.)90.00, 105.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.04905, -0.993178, 0.105794), (-0.989684, 0.034054, -0.139165), (0.134613, -0.111529, -0.984602)
Vector: 56.26168, 83.50221, 50.16138)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein ANTITHROMBIN III /


Mass: 49101.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01008

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.15 / Method: vapor diffusion, hanging drop / Details: Schreuder, H.A., (1993) J.Mol.Biol., 229, 249.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21 %beta-octyl glucoside1drop
31 mMsodium azide1drop
40.1 mMPMSF1drop
510 mMsodium phosphate1drop
618-21 %(w/v)PEG40001drop
710 mMammonium sulfate1drop
8100 mMpotassium phosphate1drop
918-21 %(w/v)PEG40001reservoir
1010 mMammonium sulfate1reservoir
11100 mMpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.2 Å / Num. obs: 17266 / % possible obs: 85.8 % / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.179 -
obs0.179 15909
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6002 0 0 0 6002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.179 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3

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