X-ray diffraction and NMR structures of aminoacyl-tRNA synthetases
(September 2003)
Arginine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Saccharomyces cerevisiae | 2.20Å | 1F7U | tRNAArg, Arginine | - | Medline |
| Thermus thermophilus | 2.30Å | 1IQ0 | - | - | Medline |
| Saccharomyces cerevisiae | 2.75Å | 1BS2 | - | - | Medline |
| Saccharomyces cerevisiae | 2.90Å | 1F7V | tRNAArg | - | Medline |
Asparagine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Escherichia coli | 2.50Å | 11AS | L-Asparagine | dimer, mutant C51A, C315Å | Medline |
| Escherichia coli | 2.20Å | 12AS | L-Asparagine, AMP | dimer, mutant C51A, C315Å | Medline |
Aspartic acid
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Saccharomyces cerevisiae | 3.00Å | 1ASY | tRNAAsp | - | Medline |
| Saccharomyces cerevisiae | 3.00Å | 1ASZ | tRNAAsp, ATP | - | Medline |
| Pyrococcus kodakaraensis | 1.90Å | 1B8A | - | - | Medline |
| Escherichia coli | 2.40Å | 1C0A | tRNAAsp, aspartyl-adenylate | - | Medline |
| Escherichia coli | 2.60Å | 1IL2 | yeast tRNAAsp, aspartyl-adenylate | - | Medline |
| Escherichia coli | 2.70Å | 1EQR | - | - | Medline |
| Thermus thermophilus | 3.00Å | 1EFW | E. coli tRNAAsp | - | Medline |
| Thermus thermophilus | 2.40Å | 1G51 | - | - | Medline |
| Thermus thermophilus | 2.30Å | 1N9W | - | archaeal type non-dicriminating | Medline |
| Thermus thermophilus | 2.01Å | 1L0W | - | space grown crystals | Medline |
| Saccharomyces cerevisiae | 2.30Å | 1EOV | - | fragment w/o 70aa N-terminal domain | Medline |
Cysteine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Escherichia coli | 2.30Å | 1LI5 | - | - | Medline |
| Escherichia coli | 2.60Å | 1LI7 | Cys | - | Medline |
Glutamine
* 5'-O-[N-(L-glutaminyl)-sulfamoyl]adenosine - active site inhibitor
Glutamic acid
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus thermophilus | 2.40Å | 1G59 | tRNAGlu | - | Medline |
| Thermus thermophilus | 1.80Å | 1J09 | Glutamic acid, ATP | - | Medline |
| Thermus thermophilus | 1.90Å | 1N75 | ATP | - | Medline |
| Thermus thermophilus | 2.40Å | 1N77 | tRNAGlu, ATP | - | Medline |
| Thermus thermophilus | 2.40Å | 1N78 | tRNAGlu, glutamol-AMP | - | Medline |
Glutamic acid - proline
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Homo sapiens | NMR | 1FYJ | - | Multifunctional peptide motif-1 | Medline |
Glycine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermotoga maritima | 1.95Å | 1J5W | - | alpha subunit | - |
| Thermus thermophilus | 2.75Å | 1ATI | - | - | Medline |
| Thermus thermophilus | 3.40Å | 1B76 | ATP | - | Medline |
| Thermus thermophilus | 3.40Å | 1GGM | glycyl-adenylate | - | Medline |
Histidine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus thermophilus | 2.70Å | 1ADJ | histidine | - | Medline |
| Thermus thermophilus | 2.80Å | 1ADY | histidyl-adenylate | - | Medline |
| Escherichia coli | 2.60Å | 1HTT | histidyl-adenylate | - | Medline |
| Escherichia coli | 2.60Å | 1KMM | histidyl-adenylate | - | Medline |
| Escherichia coli | 2.80Å | 1KMN | histidinol, ATP | - | Medline |
| Staphylococcus aureus | 2.70Å | 1QE0 | - | - | Medline |
| Thermus thermophilus | 2.40Å | 1H4V | - | - | Medline |
Isoleucine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Staphylococcus aureus | 2.20Å | 1FFY | tRNAIle, mupirocin | - | Medline |
| Thermus thermophilus | 2.50Å | 1ILE | - | - | Medline |
| Thermus thermophilus | 3.00Å | 1JZQ | isoleucyl-adenylate analogue* | - | - |
| Thermus thermophilus | 2.50Å | 1JZS | mupirocin | - | Medline |
| Escherichia coli | 2.20Å | 1QU2 | tRNAIle, mupirocin | - | - |
| Escherichia coli | 2.90Å | 1QU3 | tRNAIle, mupirocin | - | - |
* N-[isoleucinyl]-N'-[adenosyl]-diaminosulfone
Leucine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus thermophilus | 2.00Å | 1H3N | sulphamoyl analogue of leucyl-adenylate | - | Medline |
| Thermus thermophilus | 2.10Å | 1OBC | - | - | Medline |
| Thermus thermophilus | 2.20Å | 1OBH | - | - | Medline |
Lysine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Escherichia coli | 2.70Å | 1BBU | lysine | - | Medline |
| Escherichia coli | 2.70Å | 1BBW | - | - | Medline |
| Escherichia coli | 2.12Å | 1E1O | lysine | hexagonal form | Medline |
| Escherichia coli | 2.40Å | 1E1T | adenosine-5'-[lysyl-phosphate] | - | Medline |
| Escherichia coli | 2.43Å | 1E22 | lysine, ATP analogue | hexagonal form | Medline |
| Escherichia coli | 2.35Å | 1E24 | lysine, ATP | hexagonal form | Medline |
| Escherichia coli | NMR | 1KRS | - | anticodon-binding domain 40-149, average structure | Medline |
| Escherichia coli | NMR | 1KRT | - | anticodon-binding domain 40-149,
9 structures | Medline |
| Escherichia coli | 2.80Å | 1LYL | Lysine | - | Medline |
| Pyrococcus horikoshii | 2.60Å | 1IRX | - | Class I | Medline |
Methionine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Escherichia coli | NMR | 1MEA | - | zinc binding domain 138-163, average structure | Medline |
| Escherichia coli | NMR | 1MED | - | zinc binding domain 138-163,
11 structures | Medline |
| Aquifex aeolicus | 2.50Å | 1PYB | - | beta subunit | Medline |
| Escherichia coli | 1.85Å | 1F4L | methionine | - | Medline |
| Escherichia coli | 2.03Å | 1QQT | - | - | Medline |
| Pyrococcus abyssi | 2.01Å | 1MKH | - | C-Terminal Domain | Medline |
| Thermus thermophilus | 2.00Å | 1A8H | - | - | - |
Phenylalanine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus aquaticus | 2.70Å | 1B70 | phenylalanine | - | Medline |
| Thermus aquaticus | 2.50Å | 1B7Y | phenylalaninyl-adenylate | - | Medline |
| Thermus thermophilus | 2.60Å | 1JJC | phenylalanyl-adenylate | - | Medline |
| Thermus thermophilus | 3.30Å | 1EIY | tRNAPhe | - | Medline |
| Thermus thermophilus | 2.90Å | 1PYS | - | - | Medline |
Proline
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Methanocaldococcus janaschii | 3.20Å | 1NJ8 | - | - | Medline |
| Methanothermobacter thermautotrophicus | 2.55Å | 1NJ1 | cysteine sulfamoyl adenylate | - | Medline |
| Methanothermobacter thermautotrophicus | 3.11Å | 1NJ2 | - | - | Medline |
| Methanothermobacter thermautotrophicus | 2.80Å | 1NJ5 | proline sulfamoyl adenylate | - | Medline |
| Methanothermobacter thermautotrophicus | 2.85Å | 1NJ6 | alanine sulfamoyl adenylate | - | Medline |
| Thermus thermophilus | 3.00Å | 1H4Q | tRNAPro, ATP, prolinol | - | Medline |
| Thermus thermophilus | 2.85Å | 1H4S | tRNAPro, prolyl-adenylate analogue | - | Medline |
| Thermus thermophilus | 2.90Å | 1H4T | L-proline | - | Medline |
| Thermus thermophilus | 2.43Å | 1HC7 | - | - | Medline |
Serine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus thermophilus | 2.90Å | 1SER | tRNASer | - | Medline |
| Thermus thermophilus | 2.50Å | 1SES | seryl-hydroxamate-AMP | - | Medline |
| Thermus thermophilus | 2.50Å | 1SET | seryl-AMP analogue* | - | Medline |
| Thermus thermophilus | 2.50Å | 1SRY | - | - | Medline |
* 5'-O-[N-(L-seryl)-sulphamoyl]adenosine
Threonine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Escherichia coli | 2.50Å | 1EVK | threonine | truncated form 242-642 | Medline |
| Escherichia coli | 1.55Å | 1EVL | threonyl-adenylate analogue* | truncated form 242-642 | Medline |
| Escherichia coli | 1.65Å | 1FYF | seryl-adenylate analogue** | truncated form 242-642 | Medline |
| Escherichia coli | 2.90Å | 1QF6 | tRNAThr, AMP | - | Medline |
| Escherichia coli | 3.50Å | 1KOG | mRNA operator fragment | fragment 242-642 | Medline |
* 5'-O-(N-(L-threonyl)-sulfamoyl)adenosine
** 5'-O-(N-(L-seryl)-sulfamoyl)adenosine
Tryptophan
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Bacillus stearothermophilus | 2.90Å | 1D2R | - | - | Medline |
| Bacillus stearothermophilus | 1.72Å | 1I6K | tryptophanyl-5'AMP | - | Medline |
| Bacillus stearothermophilus | 1.72Å | 1I6L | tryptophanyl-5'AMP | - | Medline |
| Bacillus stearothermophilus | 1.72Å | 1I6M | tryptophanyl-5'AMP | - | Medline |
| Bacillus stearothermophilus | 2.20Å | 1M83 | ATP | closed, pre-transition state conformation | Medline |
| Bacillus stearothermophilus | 2.70Å | 1MAU | tryptophanamide, ATP | pre-transition state conformation | Medline |
| Bacillus stearothermophilus | 3.00Å | 1MAW | ATP | open conformation | Medline |
| Bacillus stearothermophilus | 2.70Å | 1MB2 | tryptophan | open conformation | Medline |
Tyrosine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Bacillus stearothermophilus | NMR | 1JH3 | - | C-terminal domain, 20 structures | Medline |
| Bacillus stearothermophilus | 2.80Å | 1TYA | - | mutant T51A | - |
| Bacillus stearothermophilus | 2.50Å | 1TYB | - | >mutant T51G | - |
| Bacillus stearothermophilus | 2.50Å | 1TYC | - | mutant T51P | - |
| Bacillus stearothermophilus | 2.50Å | 1TYD | - | mutant T51S | Medline |
| Bacillus stearothermophilus | 2.30Å | 2TS1 | tyrosinyl-adenylate | - | Medline |
| Bacillus stearothermophilus | 2.70Å | 3TS1 | tyrosinyl-adenylate | - | Medline |
| Bacillus stearothermophilus | 2.50Å | 4TS1 | tyrosine | mutant del318-417 | Medline |
| Methanococcus jannaschii | 1.95Å | 1J1U | tRNATyr, L-tyrosine | - | Medline |
| Homo sapiens | 2.21Å | 1NTG | | - | Medline |
| Staphylococcus aureus | 3.20Å | 1JII | Sb219383 | - | Medline |
| Staphylococcus aureus | 3.20Å | 1JIJ | Sb239629 | - | Medline |
| Staphylococcus aureus | 2.80Å | 1JIK | Sb243545 | - | Medline |
| Staphylococcus aureus | 2.20Å | 1JIL | Sb284485 | - | Medline |
| Thermus thermophilus | 2.90Å | 1H3E | tRNATyr, ATP, tyrosinol | - | Medline |
| Thermus thermophilus | 2.00Å | 1H3F | tyrosinol | - | Medline |
| Homo sapiens | 1.18Å | 1N3L | - | 318 aa fragment | Medline |
Valine
| Organism | Resolution | PDB | Bound molecules | Notes | Reference |
| Thermus thermophilus | 2.90Å | 1GAX | tRNAVal, valyl-adenylate analogue* | - | Medline |
| Thermus thermophilus | 2.90Å | 1IVS | tRNAVal, valyl-adenylate analogue* | - | Medline |
| Thermus thermophilus | 4.00Å | 1IYW | - | - | Medline |
* N-[valinyl]-N'-[adenosyl]-diaminosulfone