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- PDB-3gpd: TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gpd | ||||||
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Title | TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
![]() | D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE (NAD(A)-ALDEHYDE(D)) | ||||||
Function / homology | ![]() positive regulation of killing of cells of another organism => GO:0051712 / positive regulation of cytokine production => GO:0001819 / peptidyl-cysteine S-trans-nitrosylation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Watson, H.C. / Campbell, J.C. | ||||||
![]() | ![]() Title: Twinning in crystals of human skeletal muscle D-glyceraldehyde-3-phosphate dehydrogenase. Authors: Mercer, W.D. / Winn, S.I. / Watson, H.C. #1: ![]() Title: Low Resolution Structure of Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Watson, H.C. / Duee, E. / Mercer, W.D. #2: ![]() Title: The Complete Amino Acid Sequence of Human Muscle Glyceraldehyde 3-Phosphate Dehydrogenase Authors: Nowak, K. / Wolny, M. / Banas, T. | ||||||
History |
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Remark 700 | SHEET EACH SUBUNIT HAS A COFACTOR-BINDING DOMAIN AND A CATALYTIC DOMAIN. FOLLOWING THE NOMENCLATURE ...SHEET EACH SUBUNIT HAS A COFACTOR-BINDING DOMAIN AND A CATALYTIC DOMAIN. FOLLOWING THE NOMENCLATURE USED IN THE LOBSTER AND BACILLUS STEAROTHERMOPHILUS ENTRIES, THE LETTERS B AND C IN THE THREE-CHARACTER SHEET IDENTIFIERS ARE USED TO DENOTE THE APPROPRIATE DOMAIN. ASSIGNMENT OF RESIDUES TO SHEETS HAS BEEN DONE ON THE BASIS OF THE MAIN-CHAIN DIHEDRAL ANGLES (+- 25 DEGREES). RELATED HYDROGEN BONDS MAY DEVIATE SIGNIFICANTLY FROM ACCEPTED VALUES. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 93.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar 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: (-1, 0.00212, -0.00057), Vector ![]() Details | THE NON-CRYSTALLOGRAPHIC DIAD RELATING THE TWO SUBUNITS IS GIVEN ON THE MTRIX RECORDS BELOW. APPLYING THIS TRANSFORMATION TO THE RED SUBUNIT WILL YIELD APPROXIMATE COORDINATES FOR THE GREEN SUBUNIT. THIS DIAD CORRESPONDS CLOSELY TO THE CRYSTAL C-AXIS. THE TRANSFORMATION WAS DERIVED USING THE SYMMETRY AVERAGING PROCEDURE CONTAINED IN THE HENDRICKSON AND KONNERT PROGRAM. THIS CORRESPONDS TO THE R-AXIS OF THE P, Q, R SCHEME USED IN STRUCTURAL STUDIES OF OTHER SPECIES OF THE ENZYME. | |
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Components
#1: Protein | Mass: 35922.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00354, UniProt: P04406*PLUS, ![]() #2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ![]() Compound details | TURNS ARE SPECIFIED WHERE CA(N) TO CA(N+3) IS LESS THAN 5.7 ANGSTROMS AND O(N) TO N(N+3) IS LESS ...TURNS ARE SPECIFIED WHERE CA(N) TO CA(N+3) IS LESS THAN 5.7 ANGSTROMS AND O(N) TO N(N+3) IS LESS THAN 3.2 ANGSTROMS. MORE EXACT TURN DEFINITION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 % | |||||||||||||||||||||||||
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Crystal grow![]() | *PLUS pH: 5.5 / Method: microdialysis | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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Processing
Refinement | Rfactor Rwork![]() Details: THE RESOLUTION COULD BE EXTENDED TO ABOUT 1.5 ANGSTROMS USING SYNCHROTRON RADIATION. | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
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Refinement | *PLUS Highest resolution: 3.5 Å / Rfactor obs: 0.33 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |