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- PDB-2ach: CRYSTAL STRUCTURE OF CLEAVED HUMAN ALPHA1-ANTICHYMOTRYPSIN AT 2.7... -

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Basic information

Entry
Database: PDB / ID: 2ach
TitleCRYSTAL STRUCTURE OF CLEAVED HUMAN ALPHA1-ANTICHYMOTRYPSIN AT 2.7 ANGSTROMS RESOLUTION AND ITS COMPARISON WITH OTHER SERPINS
Components(ALPHA 1-ANTICHYMOTRYPSIN) x 2
KeywordsPROTEINASE INHIBITOR
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen / blood microparticle / inflammatory response / Neutrophil degranulation / extracellular space / DNA binding / extracellular exosome / extracellular region / nucleus
Similarity search - Function
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 ...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
PHOSPHATE ION / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsBaumann, U. / Huber, R. / Bode, W. / Grosse, D. / Lesjak, M. / Laurell, C.B.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Crystal structure of cleaved human alpha 1-antichymotrypsin at 2.7 A resolution and its comparison with other serpins.
Authors: Baumann, U. / Huber, R. / Bode, W. / Grosse, D. / Lesjak, M. / Laurell, C.B.
History
DepositionApr 26, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA 1-ANTICHYMOTRYPSIN
B: ALPHA 1-ANTICHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4405
Polymers45,3342
Non-polymers1,1063
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-25 kcal/mol
Surface area16260 Å2
MethodPISA
2
A: ALPHA 1-ANTICHYMOTRYPSIN
B: ALPHA 1-ANTICHYMOTRYPSIN
hetero molecules

A: ALPHA 1-ANTICHYMOTRYPSIN
B: ALPHA 1-ANTICHYMOTRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,87910
Polymers90,6674
Non-polymers2,2126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area15090 Å2
ΔGint-44 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.300, 75.300, 208.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-550-

PO4

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein ALPHA 1-ANTICHYMOTRYPSIN


Mass: 40703.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01011
#2: Protein/peptide ALPHA 1-ANTICHYMOTRYPSIN


Mass: 4630.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01011

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 87 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.7 Msodium potassium phosphate1reservoir
27 mg/mlprotein1drop
30.003 mlprecipitant1drop
45 mMphosphate1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 9999 Å / Num. obs: 14208 / % possible obs: 79 % / Observed criterion σ(I): 1.5 / Num. measured all: 61161 / Rmerge(I) obs: 0.098

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.7→8 Å
Details: THE MOST PROMINENT RAMACHANDRAN OUTLIERS ARE RESIDUES THR B 479 AND ASN A 70. PLEASE SEE REFERENCE 1 ABOVE FOR MORE INFORMATION.
RfactorNum. reflection
Rwork0.181 -
obs-13182
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 72 86 3126
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_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
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
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / Num. reflection obs: 13182 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.68
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_deg1.2

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