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- PDB-1cpj: CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cpj | ||||||
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Title | CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN | ||||||
![]() | CATHEPSIN B | ||||||
![]() | HYDROLASE / THIOL PROTEASE | ||||||
Function / homology | ![]() Trafficking and processing of endosomal TLR / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus ...Trafficking and processing of endosomal TLR / Collagen degradation / Assembly of collagen fibrils and other multimeric structures / kininogen binding / cathepsin B / response to interleukin-4 / peptidase inhibitor complex / MHC class II antigen presentation / thyroid hormone generation / cellular response to thyroid hormone stimulus / proteoglycan binding / Neutrophil degranulation / response to dexamethasone / response to amine / decidualization / collagen catabolic process / response to glucose / response to mechanical stimulus / cysteine-type peptidase activity / skeletal muscle tissue development / collagen binding / epithelial cell differentiation / proteolysis involved in protein catabolic process / response to cytokine / peptide binding / protein catabolic process / response to organic cyclic compound / sarcolemma / response to peptide hormone / autophagy / cellular response to mechanical stimulus / melanosome / peptidase activity / spermatogenesis / neuron apoptotic process / response to ethanol / endopeptidase activity / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Huber, C.P. / Jia, Z. | ||||||
![]() | ![]() Title: Crystal structures of recombinant rat cathepsin B and a cathepsin B-inhibitor complex. Implications for structure-based inhibitor design. Authors: Jia, Z. / Hasnain, S. / Hirama, T. / Lee, X. / Mort, J.S. / To, R. / Huber, C.P. #1: ![]() Title: Crystallization of Recombinant Rat Cathepsin B Authors: Lee, X. / Ahmed, F.R. / Hirama, T. / Huber, C.P. / Rose, D.R. / To, R. / Hasnain, S. / Tam, A. / Mort, J.S. | ||||||
History |
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Remark 700 | SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME ...SHEET THERE IS A BIFURCATED SHEET IN EACH MOLECULE. EACH IS REPRESENTED BY TWO SHEETS WITH SOME STRANDS IN COMMON. THUS STRANDS 4, 5, 6 OF SHEETS SA1 AND SA2 ARE IDENTICAL TO STRANDS 2, 3, 4 OF SHEETS SA2 AND SB2 IN CHAINS A AND B, RESPECTIVELY. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 107.8 KB | Display | ![]() |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.6338, 0.7386, 0.2297), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 253 B 1 .. B 253 0.457 | |
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Components
#1: Protein | Mass: 28441.562 Da / Num. of mol.: 2 / Mutation: S115A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THE V223A SUBSTITUTION WAS PRESENT IN THE PLASMID SUPPLIED TO DR. J. S. MORT BY DR. SHU CHAN ...THE V223A SUBSTITUTI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.52 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 24886 / % possible obs: 90.7 % / Rmerge(I) obs: 0.095 |
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Processing
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 Details: RESIDUE ASN 222 OF BOTH CHAINS HAS PHI-PSI ANGLES OUTSIDE THE NORMALLY PERMITTED RANGE BECAUSE ITS SIDE CHAIN OXYGEN ATOM IS INVOLVED IN A HYDROGEN BOND WITH THE ADJACENT MAIN-CHAIN N-H 223.
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Displacement parameters | Biso mean: 21.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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