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(-) Description

Title :  CRYSTAL STRUCTURE OF NMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1 IN COMPLEX WITH NIFLUMIC ACID
 
Authors :  C. Bhatia, W. W. Yue, F. Niesen, E. Pilka, E. Ugochukwu, P. Savitsky, V. H A. K. Roos, P. Filippakopoulos, F. Von Delft, T. Heightman, C. Arrows J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Date :  29 Jun 09  (Deposition) - 04 Aug 09  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Bhatia, W. W. Yue, E. Pilka, E. Ugochukwu, P. Savitsky, V. Hozjan, A. K. Roos, P. Filippakopoulos, F. Von Delft, T. Heightman, C. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, U. Oppermann
Crystal Structure Of Nmra-Like Family Domain Containing Protein 1 In Complex With Niflumic Acid
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NMRA-LIKE FAMILY DOMAIN CONTAINING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    Expression System VectorPNIC28-BSA4
    FragmentRESIDUES 1-298
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL; PROPANE-1,2,3-TRIOL
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4NFL2Ligand/Ion2-{[3-(TRIFLUOROMETHYL)PHENYL]AMINO}NICOTINIC ACID
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , THR A:13 , GLY A:14 , ALA A:15 , GLN A:16 , THR A:36 , ARG A:37 , LYS A:41 , GLY A:57 , ASP A:58 , GLN A:59 , THR A:79 , ASN A:80 , TYR A:81 , GLU A:90 , GLN A:93 , LYS A:133 , LEU A:152 , PRO A:153 , CYS A:154 , TYR A:155 , ASN A:158 , NFL A:1300 , HOH A:2033 , HOH A:2034 , HOH A:2256 , HOH A:2257 , HOH A:2258 , HOH A:2259 , HOH A:2260 , HOH A:2261 , HOH A:2262 , HOH A:2263 , HOH A:2264BINDING SITE FOR RESIDUE NAP A1299
2AC2SOFTWARETRP A:82 , HIS A:129 , CYS A:154 , ASN A:158 , HIS A:162 , PHE A:163 , TYR A:246 , LEU A:249 , GLY A:250 , PHE A:251 , LEU A:257 , MET A:260 , PHE A:261 , TYR A:264 , NAP A:1299BINDING SITE FOR RESIDUE NFL A1300
3AC3SOFTWARELYS A:5 , TYR A:73 , HIS A:107 , LEU A:120 , ARG A:151 , PHE A:263 , LEU A:266 , ASP A:269 , PO4 A:1303 , HOH A:2266 , HOH A:2267BINDING SITE FOR RESIDUE NFL A1301
4AC4SOFTWARELYS A:5 , TYR A:73 , LEU A:120 , THR A:121 , ARG A:124 , LEU A:201 , NFL A:1301 , HOH A:2268BINDING SITE FOR RESIDUE PO4 A1303
5AC5SOFTWAREARG A:218 , ARG A:270 , ASP A:271 , ILE A:272 , GLU A:273 , HOH A:2269BINDING SITE FOR RESIDUE GOL A1304
6AC6SOFTWAREALA A:72BINDING SITE FOR RESIDUE CL A1305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WM3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WM3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030689T23INMRL1_HUMANPolymorphism11557236AT23I
2UniProtVAR_030690P252LNMRL1_HUMANPolymorphism3747582AP252L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WM3)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002834291aENSE00001526041chr16:4524896-4524555342NMRL1_HUMAN-00--
1.2ENST000002834292ENSE00001293533chr16:4524167-452409474NMRL1_HUMAN1-14141A:3-1412
1.3ENST000002834293ENSE00001010612chr16:4519466-4519228239NMRL1_HUMAN14-93801A:14-9380
1.4ENST000002834294ENSE00001010610chr16:4516403-4516154250NMRL1_HUMAN94-177841A:94-17784
1.5ENST000002834295ENSE00001010609chr16:4513851-4513661191NMRL1_HUMAN177-240641A:177-24064
1.6bENST000002834296bENSE00001900515chr16:4511960-4511695266NMRL1_HUMAN241-299591A:241-29858

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:296
 aligned with NMRL1_HUMAN | Q9HBL8 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:296
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      
          NMRL1_HUMAN     3 DKKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----NmrA-2wm3A01 A:7-240                                                                                                                                                                                                                      ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..eeee....hhhhhhhhhh...eeee..hhhhh.hhhhhhhhhhhhhhhhhhhh..eeee....hhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee..ee.hhhhh....ee......eee........eeeehhhhhhhhhhhhhhhhhhhh..eee...eeehhhhhhhhhhhhhh..eee....hhhhhh....hhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L---------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2    -------------------------------------------------------------------------------Exon 1.4  PDB: A:94-177 UniProt: 94-177                                             ---------------------------------------------------------------Exon 1.6b  PDB: A:241-298 UniProt: 241-299 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.3  PDB: A:14-93 UniProt: 14-93                                           -----------------------------------------------------------------------------------Exon 1.5  PDB: A:177-240 UniProt: 177-240                       ---------------------------------------------------------- Transcript 1 (2)
                 2wm3 A   3 DKKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2WM3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WM3)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NMRL1_HUMAN | Q9HBL8)
biological process
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NMRL1_HUMAN | Q9HBL82exx 2wmd 3dxf 3e5m

(-) Related Entries Specified in the PDB File

2exx CRYSTAL STRUCTURE OF HSCARG FROM HOMO SAPIENS IN COMPLEXWITH NADP