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- PDB-1czi: CHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972 -

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Basic information

Entry
Database: PDB / ID: 1czi
TitleCHYMOSIN COMPLEX WITH THE INHIBITOR CP-113972
Components
  • CHYMOSIN
  • CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACID PROTEINASE / ASPARTYL PROTEASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


chymosin / digestion / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE / Chymosin
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGroves, M.R. / Dhanaraj, V. / Pitts, J.E. / Badasso, M. / Hoover, D. / Nugent, P. / Blundell, T.L.
Citation
Journal: Protein Eng. / Year: 1998
Title: A 2.3 A resolution structure of chymosin complexed with a reduced bond inhibitor shows that the active site beta-hairpin flap is rearranged when compared with the native crystal structure.
Authors: Groves, M.R. / Dhanaraj, V. / Badasso, M. / Nugent, P. / Pitts, J.E. / Hoover, D.J. / Blundell, T.L.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: X-Ray Analyses of Aspartic Proteinases. Iv. Structure and Refinement at 2.2 A Resolution of Bovine Chymosin
Authors: Newman, M. / Safro, M. / Frazao, C. / Khan, G. / Zdanov, A. / Tickle, I.J. / Blundell, T.L. / Andreeva, N.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Aug 9, 2023Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_initial_refinement_model / software / struct_conn / struct_ref_seq
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: CHYMOSIN
P: CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE)


Theoretical massNumber of molelcules
Total (without water)36,4032
Polymers36,4032
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-12 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.780, 132.780, 81.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11E-527-

HOH

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Components

#1: Protein CHYMOSIN / RENIN


Mass: 35672.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Description: CALF / Cell: FUNDUS / Organ: STOMACH / Production host: Escherichia coli (E. coli) / References: UniProt: P00794, chymosin
#2: Protein/peptide CP-113972 (NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE) / PFIZER INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 730.697 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: NORSTATINE-S-METHYL CYSTEINE-IODO-PHENYLALANINE-PROLINE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMsodium phosphate1reservoir
31.5 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.3→21.1 Å / Num. obs: 62777 / % possible obs: 98 % / Redundancy: 3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.2
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 1.7 / % possible all: 97.3
Reflection
*PLUS
Num. obs: 12125 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Num. measured all: 62777 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
AGROVATA/ROTAVATA(CCP4 VERSION 2.X)data reduction
AMoREphasing
RESTRAINrefinement
CCP4V 2.X (AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CMS WITHOUT LOOP 71 - 81

4cms


Resolution: 2.3→9.97 Å / σ(F): 0
Details: OTHER REFINEMENT REMARKS: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE ATOM AND HETATM RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE ...Details: OTHER REFINEMENT REMARKS: THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE ATOM AND HETATM RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. DENSITY FOR REGIONS E 156 - E 162 AND E 290 - E 292 IS POOR, AS INDICATED BY HIGHER TEMPERATURE FACTORS FOR THESE REGIONS. THE ELECTRON DENSITY FOR RESIDUES E 240 - E 244 IS NOT CONVINCING. AS A RESULT THIS REGION IS NOT PRECISELY DETERMINED. THE QUANTITY GIVEN IN THE TEMPERATURE FACTOR FIELD OF THE *ATOM* AND *HETATM* RECORDS BELOW IS U**2, WHICH IS THE MEAN-SQUARE AMPLITUDE OF ATOMIC VIBRATION. THE TEMPERATURE FACTOR, B, CAN BE DERIVED BY THE FOLLOWING RELATION - B = 8 * (PI)**2 * U**2. DENSITY FOR REGIONS E 156 - E 162 AND E 290 - E 292 IS POOR, AS INDICATED BY HIGHER TEMPERATURE FACTORS FOR THESE REGIONS. THE ELECTRON DENSITY FOR RESIDUES E 240 - E 244 IS NOT CONVINCING. AS A RESULT THIS REGION IS NOT PRECISELY DETERMINED.
RfactorNum. reflection% reflection
Rwork0.1954 --
obs-12125 98 %
Refinement stepCycle: LAST / Resolution: 2.3→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 0 191 2745
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 11988 / σ(F): 1 / Rfactor all: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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