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Yorodumi- PDB-1dr7: CRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dr7 | ||||||
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Title | CRYSTAL STRUCTURES OF ORGANOMERCURIAL-ACTIVATED CHICKEN LIVER DIHYDROFOLATE REDUCTASE COMPLEXES | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mRNA binding / mitochondrion Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Mctigue, M.A. / Davies /II, J.F. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Organomercurial-Activated Chicken Liver Dihydrofolate Reductase Complexes Authors: Mctigue, M.A. / Davies II, J.F. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J. #1: Journal: Biochemistry / Year: 1990 Title: Crystal Structures of Recombinant Human Dihydrofolate Reductase Complexed with Folate and 5-Deazafolate Authors: Davies II, J.F. / Delcamp, T.J. / Prendergast, N.J. / Ashford, V.A. / Freisheim, J.H. / Kraut, J. #2: Journal: J.Biol.Chem. / Year: 1985 Title: Refined Crystal Structure of Escherichia Coli and Chicken Liver Dihydrofolate Reductase Containing Bound Trimethoprim Authors: Matthews, D.A. / Bolin, J.T. / Burridge, J.M. / Filman, D.J. / Volz, K.W. / Kaufman, B.T. / Beddell, C.R. / Champness, J.N. / Stammers, D.K. / Kraut, J. #3: Journal: J.Biol.Chem. / Year: 1985 Title: Dihydrofolate Reductase, the Stereochemistry of Inhibitor Selectivity Authors: Matthews, D.A. / Bolin, J.T. / Burridge, J.M. / Filman, D.J. / Volz, K.W. / Kraut, J. #4: Journal: J.Biol.Chem. / Year: 1982 Title: Crystal Structure of Avian Dihydrofolate Reductase Containing Phenyltriazine and Nadph Authors: Volz, K.W. / Matthews, D.A. / Alden, R.A. / Freer, S.T. / Hansch, C. / Kaufman, B.T. / Kraut, J. #5: Journal: Biochemistry / Year: 1980 Title: Primary Structure of Chicken Liver Dihydrofolate Reductase Authors: Kumar, A.A. / Blankenship, D.T. / Kaufman, B.T. / Freisheim, J.H. | ||||||
History |
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Remark 650 | HELIX RESIDUES 21-26 (NLPWPP) FORM A LEFT-HANDED POLYPROLINE HELIX. RESIDUES LYS 108 AND VAL 109 ...HELIX RESIDUES 21-26 (NLPWPP) FORM A LEFT-HANDED POLYPROLINE HELIX. RESIDUES LYS 108 AND VAL 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E. | ||||||
Remark 700 | SHEET RESIDUES ASP 110 AND MET 111 FORM A BETA-BULGE IN STRAND E. RESIDUES VAL 115 AND GLY 116 FORM ...SHEET RESIDUES ASP 110 AND MET 111 FORM A BETA-BULGE IN STRAND E. RESIDUES VAL 115 AND GLY 116 FORM A BETA-BULGE IN STRAND E. TIGHT TURN 7 (RESIDUES 162-165) DISRUPT LAST STRAND OF SHEET INTO 2 STRANDS 8 AND 9. THIS STRAND IS CONTINUOUS IN (E. COLI). A BETA BULGE IS PRESENT HERE IN (L. CASEI). RESIDUES GLU 172 AND ILE 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dr7.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dr7.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 1dr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dr7_validation.pdf.gz | 488.3 KB | Display | wwPDB validaton report |
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Full document | 1dr7_full_validation.pdf.gz | 500.3 KB | Display | |
Data in XML | 1dr7_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1dr7_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dr/1dr7 ftp://data.pdbj.org/pub/pdb/validation_reports/dr/1dr7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 6. 2: RESIDUES 21-26 (NLPWPP) FORM LEFT-HANDED POLYPROLINE HELIX. 3: CIS PROLINE - PRO 66 4: RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E. 5: RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E. / 6: RESIDUES 115 AND 116 FORM A BETA-BULGE IN STRAND E. 7: PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION GLY 116 - GLY 117 5.680 8: TIGHT TURN 7 (RESIDUES 162-165) DISRUPT LAST STRAND OF SHEET INTO 2 STRANDS 8 AND 9. THIS STRAND IS CONTINUOUS IN E. COLI. A BETA BULGE IS PRESENT HERE IN L. CASEI. 9: RESIDUES 172 AND 175 PARTICIPATE IN BOTH TIGHT-TURN 8 AND BETA STRANDS 7 AND 9. 10: RESIDUE 200 (CALCIUM ION) LIES ON THE CRYSTALLOGRAPHIC TWO-FOLD AT ONE-HALF OCCUPANCY. | |||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21679.932 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Organ: LIVER / References: UniProt: P00378, dihydrofolate reductase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-MBO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.158 / Highest resolution: 2.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.4 Å
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Refine LS restraints |
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