[English] 日本語
![](img/lk-miru.gif)
- PDB-1gyq: CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA ME... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1gyq | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA MEXICANA IN COMPLEX WITH N6-BENZYL-NAD | ||||||
![]() | PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE) | ||||||
![]() | OXIDOREDUCTASE / OXIDOREDUCTASE (ALDEHYDE(D)-NAD+(A)) | ||||||
Function / homology | ![]() glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glycosome / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suresh, S. / Hol, W. | ||||||
![]() | ![]() Title: Structure-based design of submicromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase. Authors: Aronov, A.M. / Suresh, S. / Buckner, F.S. / Van Voorhis, W.C. / Verlinde, C.L. / Opperdoes, F.R. / Hol, W.G. / Gelb, M.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 277.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 227.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 632 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 675.4 KB | Display | |
Data in XML | ![]() | 34.4 KB | Display | |
Data in CIF | ![]() | 48.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gypS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | THERE IS ONE 222 HOMOTETRAMER PER ASYMMETRIC UNIT RESULTING IN NON-CRYSTALLOGRAPHIC 222 SYMMETRY WITHIN THE ASYMMETRIC UNIT. |
-
Components
#1: Protein | Mass: 38693.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene (production host): GLYCERALDEHYDE-3-PHOSPHATEURCE 6 DEHYDROGENASE Production host: ![]() ![]() References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NBD / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.85 % Description: DUE TO LIMITED RESOLUTION ONLY RIGID BODY REFINEMENT WAS DONE. | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: vapor diffusion, sitting drop / pH: 7.6 Details: 2UL OF SOLUTION CONTAINING 2.25 MG L. MEXICANA GAPDH, 1MM DDT, 1MM EDTA, 1MMPMSF 0.4 MM N6-BENZYL-NAD IN 10MM TRIETHANOLAMINE BUFFER PH 7.0 WAS MIXED WITH 1UL OF RESERVOIR SOLUTION ...Details: 2UL OF SOLUTION CONTAINING 2.25 MG L. MEXICANA GAPDH, 1MM DDT, 1MM EDTA, 1MMPMSF 0.4 MM N6-BENZYL-NAD IN 10MM TRIETHANOLAMINE BUFFER PH 7.0 WAS MIXED WITH 1UL OF RESERVOIR SOLUTION CONTAINING 25 %PEG5000MME, 100MM TRIS PH8.0 AND EQUILIBRATED IN SITTING DROP TRAYS, pH 7.6, VAPOR DIFFUSION, SITTING DROP | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→8 Å / Num. obs: 39118 / % possible obs: 84 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.138 / Rsym value: 13.8 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3.4→3.52 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.8 / Rsym value: 43.3 / % possible all: 83 |
Reflection shell | *PLUS % possible obs: 83 % |
-
Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1GYP Highest resolution: 3.4 Å Details: THE LIMITED RESOLUTION DID NOT PERMIT POSITIONAL OR B-FACTOR REFINEMENT. RIGID BODY REFINEMENT WAS DONE WITH X-PLOR | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.4 Å
|