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Structure paper

TitleIdentification of unknown protein function using metabolite cocktail screening.
Journal, issue, pagesStructure, Vol. 20, Page 1715-1725, Year 2012
Publish dateApr 22, 2011 (structure data deposition date)
AuthorsShumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W.
External linksStructure / PubMed:22940582
MethodsX-ray diffraction
Resolution1.51 - 2.8 Å
Structure data

PDB-3rno:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with NADP.
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3ro7:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymine.
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3roe:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine
Method: X-RAY DIFFRACTION / Resolution: 2.11 Å

PDB-3rog:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine 3'-monophosphate
Method: X-RAY DIFFRACTION / Resolution: 2.05 Å

PDB-3rox:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Theophylline
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3roz:
Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Nicotinamide
Method: X-RAY DIFFRACTION / Resolution: 2.8 Å

PDB-3rph:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+.
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-3rpz:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADPH
Method: X-RAY DIFFRACTION / Resolution: 1.51 Å

PDB-3rq2:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with NADH
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-3rq5:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+ and soaked with CoA
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-3rq6:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis soaked with ADP-ribose
Method: X-RAY DIFFRACTION / Resolution: 1.65 Å

PDB-3rq8:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis soaked with P1,P5-Di(adenosine-5') pentaphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-3rqh:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis in complex with P1,P6-Di(adenosine-5') hexaphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.75 Å

PDB-3rqq:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis in complex with P1,P3-Di(adenosine-5') triphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-3rqx:
Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis in complex with P1,P4-Di(adenosine-5') tetraphosphate
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-3rrb:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with AMP
Method: X-RAY DIFFRACTION / Resolution: 2.4 Å

PDB-3rre:
Crystal Structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ADP
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-3rrf:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ATP
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rrj:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with P1,P5-Di(adenosine-5') pentaphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-3rs8:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ADP-ribose
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rs9:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with P1,P3-Di(adenosine-5') triphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.103 Å

PDB-3rsf:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with P1,P4-Di(adenosine-5') tetraphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3rsg:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NAD.
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rsq:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADH
Method: X-RAY DIFFRACTION / Resolution: 2.054 Å

PDB-3rss:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADP
Method: X-RAY DIFFRACTION / Resolution: 1.953 Å

PDB-3rt7:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima in complex with ADP-glucose
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rt9:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Coenzyme A
Method: X-RAY DIFFRACTION / Resolution: 1.952 Å

PDB-3rta:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Acetyl Coenzyme A
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-3rtb:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Adenosine-3'-5'-Diphosphate
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rtc:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NAD and ATP.
Method: X-RAY DIFFRACTION / Resolution: 2.101 Å

PDB-3rtd:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADH and ADP.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-3rte:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADP and ATP.
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-3rtg:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with Coenzyme A and ATP
Method: X-RAY DIFFRACTION / Resolution: 2.052 Å

PDB-3ru2:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADPH.
Method: X-RAY DIFFRACTION / Resolution: 2.2 Å

PDB-3ru3:
Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADPH and ATP.
Method: X-RAY DIFFRACTION / Resolution: 2.605 Å

Chemicals

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

ChemComp-HOH:
WATER

ChemComp-TDR:
THYMINE

ChemComp-SO4:
SULFATE ION

ChemComp-THM:
THYMIDINE

ChemComp-T3P:
THYMIDINE-3'-PHOSPHATE

ChemComp-TEP:
THEOPHYLLINE

ChemComp-NCA:
NICOTINAMIDE / medication*YM

ChemComp-MG:
Unknown entry

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-NPW:
BETA-6-HYDROXY-1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE

ChemComp-NAX:
BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

ChemComp-COA:
COENZYME A

ChemComp-GOL:
GLYCEROL

ChemComp-APR:
ADENOSINE-5-DIPHOSPHORIBOSE

ChemComp-AP5:
BIS(ADENOSINE)-5'-PENTAPHOSPHATE

ChemComp-B6P:
P1,P6-Di(adenosine-5') hexaphosphate

ChemComp-BA3:
BIS(ADENOSINE)-5'-TRIPHOSPHATE

ChemComp-B4P:
BIS(ADENOSINE)-5'-TETRAPHOSPHATE

ChemComp-CL:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE

ChemComp-ADQ:
ADENOSINE-5'-DIPHOSPHATE-GLUCOSE

ChemComp-ACO:
ACETYL COENZYME *A

ChemComp-A3P:
ADENOSINE-3'-5'-DIPHOSPHATE

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Source
  • mus musculus (house mouse)
  • bacillus subtilis (bacteria)
  • thermotoga maritima (bacteria)
  • escherichia coli (E. coli)
KeywordsPROTEIN BINDING / ROSSMANN FOLD / lyase/lyase substrate / STRUCTURAL GENOMICS / PSI-biology / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / LYASE / lyase-lyase substrate complex / Unknown function / ADP/ATP-dependent NAD(P)H-hydrate dehydratase

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