[English] 日本語
![](img/lk-miru.gif)
- PDB-1c2t: NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1c2t | ||||||
---|---|---|---|---|---|---|---|
Title | NEW INSIGHTS INTO INHIBITOR DESIGN FROM THE CRYSTAL STRUCTURE AND NMR STUDIES OF E. COLI GAR TRANSFORMYLASE IN COMPLEX WITH BETA-GAR AND 10-FORMYL-5,8,10-TRIDEAZAFOLIC ACID. | ||||||
![]() | GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE | ||||||
![]() | TRANSFERASE / PURINE BIOSYNTHESIS / ANTI-CANCER AGENT / INHIBITOR COMPLEX | ||||||
Function / homology | ![]() phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process / DNA damage response / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Greasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A. | ||||||
![]() | ![]() Title: New insights into inhibitor design from the crystal structure and NMR studies of Escherichia coli GAR transformylase in complex with beta-GAR and 10-formyl-5,8,10-trideazafolic acid. Authors: Greasley, S.E. / Yamashita, M.M. / Cai, H. / Benkovic, S.J. / Boger, D.L. / Wilson, I.A. #1: ![]() Title: A pH-dependent stabilization of an active site loop observed from low and high pH crystal structures of mutant monomeric glycinamide ribonucleotide transformylase at 1.8-1.9A Authors: Su, Y. / Yamashita, M.M. / Greasley, S.E. / Mullen, C.A. / Shim, J.H. / Jennings, P.A. / Benkovic, S.J. / Wilson, I.A. #2: ![]() Title: 10-Formyl-5,8,10-trideazafolic acid (10-formyl-TDAF): a potent inhibitor of glycinamide ribonucleotide transformylase. Authors: Boger, D.L. / Haynes, N.-E. / Kitos, P.A. / Warren, J. / Ramcharan, J. / Marolewski, A.E. / Benkovic, S.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 98.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 23.8 KB | Display | |
Data in CIF | ![]() | 31.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23266.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08179, phosphoribosylglycinamide formyltransferase 1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG 3350, IMIDAZOLE MALATE, CALCIUM CHLORIDE, MPD, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 22.0K, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 94 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 10, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 23742 / Num. obs: 23742 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.421 / Num. unique all: 2338 / % possible all: 99.3 |
Reflection | *PLUS |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 99.3 % / Num. unique obs: 2338 / Mean I/σ(I) obs: 1.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 471792.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|