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Structure paper

TitleCrystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Journal, issue, pagesTo Be Published
Publish dateMar 13, 2015 (structure data deposition date)
AuthorsElkins, P.A. / Bonnette, W.G. / Williams, S.P. / Stuckey, J.A.
External linksSearch PubMed
MethodsX-ray diffraction
Resolution1.45 - 2.65 Å
Structure data

PDB-4ypw:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.311 Å

PDB-4ypx:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-4ypy:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4ypz:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.84 Å

PDB-4yq0:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-4yq2:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.65 Å

PDB-4yq3:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.49 Å

PDB-4yq4:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-4yq5:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-4yq6:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-4yq7:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-4yq8:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-4yq9:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.64 Å

PDB-4yqa:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-4yqb:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-4yqc:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.89 Å

PDB-4yqd:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-4yqg:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.858 Å

PDB-4yqi:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-4yqj:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.94 Å

PDB-4yqk:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.83 Å

PDB-4yql:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.401 Å

PDB-4yqn:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-4yqo:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-4yqp:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 2.601 Å

PDB-4yqq:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-4yqr:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.701 Å

PDB-4yqs:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.902 Å

PDB-4yqt:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-5d9f:
Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Method: X-RAY DIFFRACTION / Resolution: 1.91 Å

Chemicals

ChemComp-4FD:
6-(benzylamino)pyridine-3-carboxamide

ChemComp-HOH:
WATER

ChemComp-4FG:
6-aminopyridine-3-carboxamide

ChemComp-4F9:
4-(1H-imidazol-5-yl)pyridine

ChemComp-FLC:
CITRATE ANION

ChemComp-4FL:
4-(1H-imidazol-2-yl)pyridine

ChemComp-4FM:
4-amino-N-(4-chlorobenzyl)-1,2,5-oxadiazole-3-carboxamide

ChemComp-EFY:
N-(1-{[(3-tert-butylbenzoyl)amino]methyl}cyclopentyl)-2,1-benzoxazole-4-carboxamide

ChemComp-4G1:
N-(1-{[(3-methylbenzoyl)amino]methyl}cyclopentyl)-2,1-benzoxazole-4-carboxamide

ChemComp-4G3:
6-[(3-hydroxybenzyl)amino]pyridine-3-carboxamide

ChemComp-4G0:
6-{[3-(dimethylamino)benzyl]amino}pyridine-3-carboxamide

ChemComp-4FX:
6-[(2-methoxybenzyl)amino]pyridine-3-carboxamide

ChemComp-4G4:
6-{[2-(dimethylamino)benzyl]amino}pyridine-3-carboxamide

ChemComp-4FV:
4-amino-N-[(1R,3S)-3-hydroxycyclopentyl]-1,2,5-oxadiazole-3-carboxamide

ChemComp-4GO:
6-(cyclopentylamino)pyridine-3-carboxamide

ChemComp-4GN:
6-[(cyclopentylmethyl)amino]pyridine-3-carboxamide

ChemComp-4GM:
6-[(2-hydroxybenzyl)amino]pyridine-3-carboxamide

ChemComp-EFW:
6-{[(1R,3R)-3-hydroxycyclopentyl]amino}pyridine-3-carboxamide

ChemComp-4GZ:
6-{[(1-{2-[(3-methylbenzoyl)amino]ethyl}cyclohexyl)methyl]amino}pyridine-3-carboxamide

ChemComp-4GY:
4-amino-N-(cyclohexylmethyl)-1,2,5-oxadiazole-3-carboxamide

ChemComp-4GX:
(4-amino-1,2,5-oxadiazol-3-yl)[4-(pyridin-2-ylmethyl)piperazin-1-yl]methanone

ChemComp-4GT:
4-amino-2-(cyclopentylamino)pyrimidine-5-carboxamide

ChemComp-4GS:
4-amino-N-(piperidin-4-yl)-1,2,5-oxadiazole-3-carboxamide

ChemComp-4H4:
4-amino-N-[(1S,2R)-2-(4-sulfamoylphenyl)cyclopropyl]-1,2,5-oxadiazole-3-carboxamide

ChemComp-4H3:
6-{[(1R,3S,4R)-3-hydroxy-4-(hydroxymethyl)cyclopentyl]amino}pyridine-3-carboxamide

ChemComp-4H1:
6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide

ChemComp-4H6:
6-{[2-(morpholin-4-yl)benzyl]amino}pyridine-3-carboxamide

ChemComp-4H7:
6-{[2-(4-methylpiperazin-1-yl)benzyl]amino}pyridine-3-carboxamide

ChemComp-4HQ:
(4-amino-1,2,5-oxadiazol-3-yl)(4-methylpiperazin-1-yl)methanone

ChemComp-4H9:
(5-amino-1H-1,2,4-triazol-1-yl)(4-methoxyphenyl)methanone

ChemComp-4H8:
4-amino-2-[(2,2-dimethylpropyl)amino]pyrimidine-5-carboxamide

ChemComp-58G:
6-{[(1R,3S)-3-phenylcyclopentyl]amino}pyridine-3-carboxamide

Source
  • haemophilus influenzae (strain atcc 51907 / dsm 11121 / kw20 / rd) (bacteria)
  • haemophilus influenzae (bacteria)
Keywordstransferase/transferase inhibitor / TrmD / Haemophilus influenzae / SAM-binding / knot / transferase-transferase inhibitor complex / Dimerization / Models / tRNA Methyltransferases / S-adenosyl methionine

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