[English] 日本語
![](img/lk-miru.gif)
- PDB-4mdh: REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4mdh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION | |||||||||
![]() | CYTOPLASMIC MALATE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE(NAD(A)-CHOH(D)) | |||||||||
Function / homology | ![]() diiodophenylpyruvate reductase / hydroxyphenylpyruvate reductase activity / Gluconeogenesis / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / NAD binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Birktoft, J.J. / Banaszak, L.J. | |||||||||
![]() | ![]() Title: Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution. Authors: Birktoft, J.J. / Rhodes, G. / Banaszak, L.J. #1: ![]() Title: Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenase Authors: Birktoft, J.J. / Fu, Z. / Carnahan, G.E. / Rhodes, G. / Roderick, S.L. / Banaszak, L.J. #2: ![]() Title: Structure of Porcine Heart Cytoplasmic Malate Dehydrogenase. Combining X-Ray Diffraction and Chemical Sequence Data in Structural Studies Authors: Birktoft, J.J. / Bradshaw, R.A. / Banaszak, L.J. #3: ![]() Title: The Presence of a Histidine-Aspartic Acid Pair in the Active Site of 2-Hydroxyacid Dehydrogenases. X-Ray Refinement of Cytoplasmic Malate Dehydrogenase Authors: Birktoft, J.J. / Banaszak, L.J. #4: ![]() Title: The Interactions of Nad/Nadh with 2-Hydroxy Acid Dehydrogenases Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J. #5: ![]() Title: Amino Acid Sequence Homology Among the 2-Hydroxy Acid Dehydrogenases. Mitochondrial and Cytoplasmic Malate Dehydrogenases Form a Homologous System with Lactate Dehydrogenase Authors: Birktoft, J.J. / Fernley, R.T. / Bradshaw, R.A. / Banaszak, L.J. #6: ![]() Year: 1975 Title: Nicotinamide Adenine Dinucleotide and the Active Site of Cytoplasmic Malate Dehydrogenase Authors: Banaszak, L.J. / Webb, L.E. #7: ![]() Title: Conformation of Nicotinamide Adenine Dinucleotide Bound to Cytoplasmic Malate Dehydrogenase Authors: Webb, L.E. / Hill, E.J. / Banaszak, L.J. #8: ![]() Title: Polypeptide Conformation of Cytoplasmic Malate Dehydrogenase from an Electron Density Map at 3.0 Angstroms Resolution Authors: Hill, E. / Tsernoglou, D. / Webb, L. / Banaszak, L.J. #9: ![]() Title: The Identification of an Asymmetric Complex of Nicotinamide Adenine Dinucleotide and Pig Heart Cytoplasmic Malate Dehydrogenase Authors: Glatthaar, B.E. / Banaszak, L.J. / Bradshaw, R.A. #10: ![]() Title: Cytoplasmic Malate Dehydrogenase-Heavy Atom Derivatives and Low Resolution Structure Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J. #11: ![]() Title: Structural Studies on Heart Muscle Malate Dehydrogenases Authors: Tsernoglou, D. / Hill, E. / Banaszak, L.J. | |||||||||
History |
| |||||||||
Remark 700 | SHEET IN SHEET S2 THE REGULAR HYDROGEN BONDING PATTERN IS DISRUPTED BY A THREE RESIDUE BULGE ...SHEET IN SHEET S2 THE REGULAR HYDROGEN BONDING PATTERN IS DISRUPTED BY A THREE RESIDUE BULGE (RESIDUES 194 -196) IN STRAND 2. IN SHEET S1 A BETA BULGE IS FOUND IN STRAND 1 AT RESIDUE 64. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 122.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 971.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 38.6 KB | Display | |
Data in CIF | ![]() | 54.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: RESIDUES PRO A 131 AND PRO B 131 ARE CIS PROLINES. / 2: SEE REMARK 5. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.86554, 0.46781, -0.17888), Vector: |
-
Components
#1: Protein | Mass: 36393.980 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | THREE DIFFERENT COMPOUNDS CONTAINING HEAVY ATOMS WERE FOUND TO BIND TO CMDH. EACH ASYMMETRIC UNIT ...THREE DIFFERENT COMPOUNDS CONTAINING | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % |
---|
-Data collection
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 6 Å / Num. all: 23373 / Num. obs: 22910 |
---|
-
Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→6 Å / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→6 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 22910 / Rfactor obs: 0.167 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|