Learn how to use Swiss-PdbViewer. Work through sections 1-4 of the Swiss-PdbViewer Tutorial.
Under construction. Last revision 2006/10/27.
This page contains links to PDB models of proteins with bound ligands of all types, including cofactors, prosthetic groups, inhibitors, and metal ions, and in some cases, substrates. These molecules listed in HETATM lines of PDB files, and are sometimes called HETATM or HET groups. This term has come to refer to any non-protein component of a protein model.
To use DeepView to see the ligand in the protein model listed, use the File:Import command and enter the PDB code listed in the left column.
To see some other tools for viewing and analyzing structure, click the PDB code in the left column. On the PDB Structure Summary page, find Chemical Component, and click on Ligand Interaction to see the ligand and analyze its contacts with the protein. The graphics viewers are Java applets, so your computer needs to have up-to-date Java tools.
TEACHERS: Looking for good subjects for graphics projects? USM Biochemistry students have successfully used all of the models listed here in Assignment 1 in the DeepView Tutorial.
|
Protein |
|
PDB Ligand Code |
Phthalate dioxygenase reductase |
FMN |
FMN | |
Adenylate kinase |
ATP-analog inhibitor AP5A in two conformations |
AP5 | |
DNA (cytosine-C5-)-methyl transferase |
S-adenosylmethionine |
SAM | |
Citrate synthase |
Coenzyme A Citrate |
COA CIT |
|
Transketolase |
Thiamine pyrophosphate Calcium |
TPP CA |
|
Aspartate aminotransferase |
Pyridoxal phosphate |
PLP | |
Adipocyte lipid-binding protein |
Oleic acid |
OLA | |
Avidin |
Biotin N-acetyl-D-glucosamine |
BTN NAG |
|
Phosphoenol pyruvate carboxykinase |
ATP Magnesium ion Oxalate ion |
ATP MG OXL |
|
Methionine synthase |
Vitamin B12 |
COB | |
H-protein of glycine cleavage system |
Lipoic acid |
LPA | |
Cellular retinol-binding protein |
Retinol |
RTL | |
Dihydrofolate reductase |
Folic acid |
FOL | |
Flavodoxin |
FMN |
FMN | |
Acetyl-CoA carboxylase |
Biotin |
BTN | |
Allophycocyanin |
Phycocyanobilin |
||
HIV-1 protease |
Sulfamide inhibitor AHA006 |
NMB | |
Alpha-thrombin |
Peptide-analog inhibitor |
No HETATM ligand present. The "ligand" is a small polypeptide, so it is listed as a separate protein chain. | |
Dihydrofolate reductase |
NADP |
NAP | |
Lactate dehydrogenase |
NAD |
NAD | |
Glutathione reductase |
FAD |
FAD | |
T-cell signal-transduction molecule SAP (two chains [A & C] and two polypeptide ligands [listed as chains B & D] |
Phosphopeptide binding target |
No HETATM ligand present. The "ligand" is a small polypeptide, so it is listed as a separate protein chain (B or D). It contains the unusual residue PTR (phosphotyrosine). | |
Ras protein catalytic domain |
GDP |
GDP | |
ATP-binding cassette (ABC) transporter protein |
Mg-ADP |
ATP and MG | |
Biliverdin IX Reductase |
NADP Meso-biliverdin |
NAP MBV |
|
Rab4A, Ras-related protein |
GDP |
GDP | |
Cytochrome C-500 |
Heme C |
HEC | |
Peptide deformylase |
Sb-543668, a potential pneumonia drug (2 superimposed models in alternative conformations) |
SB8 |
|
| 1DB1 | Nuclear receptor for vitamin D | Vitamin D | VDX |
| 1ASH | Hemoglobin from the nematode Ascaris suum | Iron-Heme (protoporphyrin 9) | HEM |
| 1S8G | Phospholipase A2 | Dodecanoic acid (lauric acid) | LAU |
GFP-like fluorescent protein |
Fluorophore, made from modified residues 68, 69, & 70, listed in file after residue 67 as as CR7 68 (covalently bound, but peptide bonds might not be drawn -- find them). Shown in two alternative conformations. |
CR7 |
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