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- PDB-8dfr: REFINED CRYSTAL STRUCTURES OF CHICKEN LIVER DIHYDROFOLATE REDUCTA... -
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Basic information
Entry | Database: PDB / ID: 8dfr | ||||||
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Title | REFINED CRYSTAL STRUCTURES OF CHICKEN LIVER DIHYDROFOLATE REDUCTASE. 3 ANGSTROMS APO-ENZYME AND 1.7 ANGSTROMS NADPH HOLO-ENZYME COMPLEX | ||||||
![]() | DIHYDROFOLATE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE(CHNH(D)-NAD+ OR NADP+(A)) | ||||||
Function / homology | ![]() tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding ...tetrahydrofolate metabolic process / response to methotrexate / dihydrofolate metabolic process / glycine biosynthetic 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Matthews, D.A. / Oatley, S.J. / Burridge, J. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J. | ||||||
![]() | ![]() Title: Refined Crystal Structures of Chicken Liver Dihydrofolate Reductase. 3 Angstroms Apo-Enzyme and 1.7 Angstroms Nadph Holo-Enzyme Complex Authors: Davies /II, J.F. / Matthews, D.A. / Oatley, S.J. / Kaufman, B.T. / Xuong, N.-H. / Kraut, J. #1: ![]() Title: Refined Crystal Structures 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. #2: ![]() 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. #3: ![]() 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. #4: ![]() 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 THROUGH 26 FORM A NEARLY-IDEAL LEFT-HANDED POLYPROLINE HELIX WITH SEQUENCE ASN- ...HELIX RESIDUES 21 THROUGH 26 FORM A NEARLY-IDEAL LEFT-HANDED POLYPROLINE HELIX WITH SEQUENCE ASN-LEU-PRO-TRP-PRO-PRO. RESIDUE 102 PARTICIPATES IN BOTH HELIX E AND HELIX EP. RESIDUES 108 AND 109 PARTICIPATE IN BOTH HELIX EP AND BETA STRAND E. | ||||||
Remark 700 | SHEET THIS PROTEIN CONTAINS ONE EIGHT-STRANDED SHEET. THE LAST STRAND IS INTERRUPTED BY A BETA- ...SHEET THIS PROTEIN CONTAINS ONE EIGHT-STRANDED SHEET. THE LAST STRAND IS INTERRUPTED BY A BETA-BLOWOUT OF EIGHT RESIDUES, FOUR OF WHICH (162 - 165) FORM A BETA-TURN. THIS IS REPRESENTED BY PRESENTING THE SHEET TWICE WITH DIFFERENT LAST STRANDS. IN E. COLI DFR THIS STRAND IS CONTINUOUS. IN L. CASEI DFR A BETA BULGE IS PRESENT. RESIDUES 172 AND 175 PARTICIPATE IN BOTH TIGHT TURN 8 AND BETA STRANDS 7 AND 9. RESIDUES 115 AND 116 FORM A BETA-BULGE IN STRAND E. RESIDUES 110 AND 111 FORM A BETA-BULGE IN STRAND E. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 56.4 KB | Display | ![]() |
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PDB format | ![]() | 40 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 473.2 KB | Display | ![]() |
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Full document | ![]() | 487.5 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Atom site foot note | 1: RESIDUE 66 IS A CIS PROLINE. 2: THE PEPTIDE BOND JOINING RESIDUES GLY 116 AND GLY 117 IS IN THE CIS CONFORMATION. | ||||||||
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.) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.67 % |
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Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.188 / Highest resolution: 1.7 Å Details: CYS 11 APPEARS TO BE OXIDIZED TO SO3H (CYSTEIC ACID) DURING X-RAY DATA COLLECTION. CYSTEIC ACID WAS APPROXIMATED BY PLACING THREE WATER MOLECULES (HOH 645, HOH 657, AND HOH 674) AROUND THE ...Details: CYS 11 APPEARS TO BE OXIDIZED TO SO3H (CYSTEIC ACID) DURING X-RAY DATA COLLECTION. CYSTEIC ACID WAS APPROXIMATED BY PLACING THREE WATER MOLECULES (HOH 645, HOH 657, AND HOH 674) AROUND THE SULFUR OF THE CYSTEINE RESIDUE. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.7 Å
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Refine LS restraints |
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