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Structure paper

TitleA fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis
Journal, issue, pagesComput Struct Biotechnol J, Vol. 19, Page 3491-3506, Year 2021
Publish dateFeb 22, 2021 (structure data deposition date)
AuthorsGupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. ...Gupta, P. / Thomas, S.E. / Zaidan, S.A. / Pasillas, M.A. / Cory-Wright, J. / Sebastian-Perez, V. / Burgess, A. / Cattermole, E. / Meghir, C. / Abell, C. / Coyne, A.G. / Jacobs, W.R. / Blundell, T.L. / Tiwari, S. / Mendes, V.
External linksComput Struct Biotechnol J / Search PubMed
MethodsX-ray diffraction
Resolution1.47 - 2.81 Å
Structure data

PDB-7nlf:
Crystal structure of Mycobacterium tuberculosis ArgB in apo form.
Method: X-RAY DIFFRACTION / Resolution: 2.08 Å

PDB-7nln:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with N-acetyl-glutamate
Method: X-RAY DIFFRACTION / Resolution: 1.92 Å

PDB-7nlo:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with L-arginine
Method: X-RAY DIFFRACTION / Resolution: 1.82 Å

PDB-7nlp:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with L-canavanine
Method: X-RAY DIFFRACTION / Resolution: 2.213 Å

PDB-7nlq:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-(isoxazol-5-yl)phenol
Method: X-RAY DIFFRACTION / Resolution: 2.497 Å

PDB-7nlr:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-phenyl-1H-imidazole
Method: X-RAY DIFFRACTION / Resolution: 2.254 Å

PDB-7nls:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with methyl 4-hydroxy-3-iodobenzoate
Method: X-RAY DIFFRACTION / Resolution: 2.648 Å

PDB-7nlt:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 4-(4-methylpiperazin-1-yl)benzoic acid
Method: X-RAY DIFFRACTION / Resolution: 2.225 Å

PDB-7nlu:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1-(1H-indol-3-yl)ethan-1-one
Method: X-RAY DIFFRACTION / Resolution: 2.235 Å

PDB-7nlw:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-(5-methoxy-1H-indol-3-yl)acetonitrile
Method: X-RAY DIFFRACTION / Resolution: 2.32 Å

PDB-7nlx:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 7-(trifluoromethyl)quinolin-4-ol.
Method: X-RAY DIFFRACTION / Resolution: 2.234 Å

PDB-7nly:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2-Chlorobenzimidazole.
Method: X-RAY DIFFRACTION / Resolution: 2.246 Å

PDB-7nlz:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 5-Methoxy-6-(trifluoromethyl)indole.
Method: X-RAY DIFFRACTION / Resolution: 2.163 Å

PDB-7nm0:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1-(2,6-dihydroxyphenyl)ethan-1-one.
Method: X-RAY DIFFRACTION / Resolution: 2.281 Å

PDB-7nn1:
Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate
Method: X-RAY DIFFRACTION / Resolution: 1.54 Å

PDB-7nn4:
Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal 5'-phosphate and 3-hydroxy-2-naphthoic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.47 Å

PDB-7nn7:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with dimethyl 5-hydroxyisophthalate.
Method: X-RAY DIFFRACTION / Resolution: 2.172 Å

PDB-7nn8:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 1H-indole-3-carbonitrile.
Method: X-RAY DIFFRACTION / Resolution: 2.267 Å

PDB-7nnb:
Crystal structure of Mycobacterium tuberculosis ArgB in complex with 2,8-bis(trifluoromethyl)quinolin-4-ol.
Method: X-RAY DIFFRACTION / Resolution: 2.186 Å

PDB-7nnc:
Crystal structure of Mycobacterium tuberculosis ArgD with prosthetic group pyridoxal-5'-phosphate and 6-Methoxyquinoline-3-carboxylic acid
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7nnf:
Crystal structure of Mycobacterium tuberculosis ArgF in apo form.
Method: X-RAY DIFFRACTION / Resolution: 1.52 Å

PDB-7nni:
Crystal structure of Mycobacterium tuberculosis ArgC apoenzyme
Method: X-RAY DIFFRACTION / Resolution: 1.544 Å

PDB-7nnq:
Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+)
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

PDB-7nnr:
Crystal structure of Mycobacterium tuberculosis ArgC in complex with xanthene-9-carboxylic acid
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-7nnv:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with carbamoyl phosphate.
Method: X-RAY DIFFRACTION / Resolution: 1.67 Å

PDB-7nnw:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with methyl 4-hydroxy-3-iodobenzoate.
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-7nny:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with naphthalen-1-ol.
Method: X-RAY DIFFRACTION / Resolution: 1.57 Å

PDB-7nnz:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with 5-methyl-4-phenylthiazol-2-amine.
Method: X-RAY DIFFRACTION / Resolution: 1.68 Å

PDB-7nor:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with 2-fluoro-4-hydroxybenzonitrile.
Method: X-RAY DIFFRACTION / Resolution: 1.59 Å

PDB-7nos:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with 4-bromo-6-(trifluoromethyl)-1H-benzo[d]imidazole.
Method: X-RAY DIFFRACTION / Resolution: 1.77 Å

PDB-7not:
Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine dinucleotide phosphate (NADP+) and 5-Methoxy-3-indoleacetic acid
Method: X-RAY DIFFRACTION / Resolution: 2.54 Å

PDB-7nou:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with (3,5-dichlorophenyl)boronic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

PDB-7nov:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with (4-methyl-3-nitrophenyl)boronic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-7np0:
Crystal structure of Mycobacterium tuberculosis ArgF in complex with (4-nitrophenyl)boronic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.76 Å

PDB-7nph:
Crystal structure of Mycobacterium tuberculosis ArgC in complex with 5-methoxy-1,3-benzoxazole-2-carboxylic acid
Method: X-RAY DIFFRACTION / Resolution: 2.57 Å

PDB-7npj:
Crystal structure of Mycobacterium tuberculosis ArgC in complex with 6-phenoxy-3-pyridinamine
Method: X-RAY DIFFRACTION / Resolution: 2.81 Å

Chemicals

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-NLG:
N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid

ChemComp-ARG:
ARGININE / Arginine

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM / CHES (buffer)

ChemComp-GGB:
L-CANAVANINE / Canavanine

ChemComp-97T:
2-(1,2-oxazol-5-yl)phenol

ChemComp-PIY:
2-phenyl-1H-imidazole

ChemComp-98T:
methyl 3-iodanyl-4-oxidanyl-benzoate

ChemComp-14N:
4-(4-methylpiperazin-1-yl)benzoic acid

ChemComp-5RN:
1-(1~{H}-indol-3-yl)ethanone

ChemComp-UOK:
2-(5-methoxy-1~{H}-indol-3-yl)ethanenitrile

ChemComp-97W:
7-(trifluoromethyl)quinolin-4-ol

ChemComp-98K:
2-chloranyl-1~{H}-benzimidazole

ChemComp-98Q:
5-methoxy-6-(trifluoromethyl)-1~{H}-indole

ChemComp-9EQ:
1-[2,6-bis(oxidanyl)phenyl]ethanone

ChemComp-NO3:
NITRATE ION / Nitrate

ChemComp-BZJ:
3-hydroxynaphthalene-2-carboxylic acid / 3-Hydroxy-2-naphthoic acid

ChemComp-98W:
dimethyl 5-oxidanylbenzene-1,3-dicarboxylate

ChemComp-98Z:
1~{H}-indole-3-carbonitrile

ChemComp-97Q:
2,8-bis(trifluoromethyl)quinolin-4-ol

ChemComp-UMH:
6-methoxyquinoline-3-carboxylic acid

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

ChemComp-BTB:
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM / Bis-tris methane

ChemComp-UJQ:
9~{H}-xanthene-9-carboxylic acid

ChemComp-CP:
PHOSPHORIC ACID MONO(FORMAMIDE)ESTER / Carbamoyl phosphate

ChemComp-1NP:
1-NAPHTHOL / 1-Naphthol

ChemComp-PTZ:
5-methyl-4-phenyl-1,3-thiazol-2-amine

ChemComp-8H8:
2-fluoro-4-hydroxybenzonitrile

ChemComp-UJZ:
4-bromanyl-6-(trifluoromethyl)-1~{H}-benzimidazole

ChemComp-MYI:
(5-methoxy-1H-indol-3-yl)acetic acid

ChemComp-NMR:
[3,5-bis(chloranyl)phenyl]-oxidanyl-oxidanylidene-boron

ChemComp-UK2:
(4-methyl-3-nitro-phenyl)-oxidanyl-oxidanylidene-boron

ChemComp-UKH:
p-nitrophenylboronic acid

ChemComp-UKE:
5-methoxy-1,3-benzoxazole-2-carboxylic acid

ChemComp-UKK:
6-phenoxy-3-pyridinamine

Source
  • mycobacterium tuberculosis h37rv (bacteria)
  • mycobacterium tuberculosis (strain atcc 25618 / h37rv) (bacteria)
KeywordsTRANSFERASE / ArgB Acetylglutamate kinase / ArgB / Acetylglutamate kinase / ArgD / N-acetylornithine aminotrasferase / AcOAT / ArgF / Ornithine Carbamoyltransferase / OXIDOREDUCTASE / ArgC / N-acetyl-gamma-glutamyl-phosphate reductase / NAGPR / Arginine biosynthesis

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