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(-) Description

Title :  THE CRYSTALLOGRAPHIC STRUCTURE OF A HUMAN DIHYDROPTERIDINE REDUCTASE NADH BINARY COMPLEX EXPRESSED IN ESCHERICHIA COLI BY A CDNA CONSTRUCTED FROM ITS RAT HOMOLOGUE
 
Authors :  K. I. Varughese, Y. Su, N. H. Xuong, J. M. Whiteley
Date :  18 Aug 93  (Deposition) - 31 Aug 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Oxidoreductase(Acting On Nadh) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Su, K. I. Varughese, N. H. Xuong, T. L. Bray, D. J. Roche, J. M. Whitele
The Crystallographic Structure Of A Human Dihydropteridine Reductase Nadh Binary Complex Expressed In Escherichia Coli By A Cdna Constructed From Its Rat Homologue.
J. Biol. Chem. V. 268 26836 1993
PubMed-ID: 8262916

(-) Compounds

Molecule 1 - DIHYDROPTERIDINE REDUCTASE
    ChainsA
    EC Number1.6.99.7
    EngineeredYES
    GeneCDNA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:15 , GLY A:16 , ARG A:18 , GLY A:19 , ALA A:20 , LEU A:21 , VAL A:39 , ASP A:40 , VAL A:53 , LYS A:72 , VAL A:85 , ALA A:86 , GLY A:87 , GLY A:88 , THR A:113 , ALA A:134 , TYR A:149 , LYS A:153 , PRO A:181 , VAL A:182 , THR A:183 , LEU A:184 , ASN A:189 , HOH A:247 , HOH A:249 , HOH A:252BINDING SITE FOR RESIDUE NAD A 244

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HDR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HDR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (17, 17)

Asymmetric Unit (17, 17)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_008121L14PDHPR_HUMANDisease (HPABH4C)756639609AL13P
02UniProtVAR_021767G17RDHPR_HUMANDisease (HPABH4C)757483045AG16R
03UniProtVAR_008122G17VDHPR_HUMANDisease (HPABH4C)  ---AG16V
04UniProtVAR_021768G18DDHPR_HUMANDisease (HPABH4C)  ---AG17D
05UniProtVAR_006960G23DDHPR_HUMANDisease (HPABH4C)104893863AG22D
06UniProtVAR_006961W36RDHPR_HUMANDisease (HPABH4C)104893865AW35R
07UniProtVAR_013027S51TDHPR_HUMANPolymorphism  ---AS50T
08UniProtVAR_021769Q66RDHPR_HUMANDisease (HPABH4C)  ---AQ65R
09UniProtVAR_006962L74PDHPR_HUMANDisease (HPABH4C)  ---AL73P
10UniProtVAR_006963W108GDHPR_HUMANDisease (HPABH4C)104893864AW107G
11UniProtVAR_006965P145LDHPR_HUMANDisease (HPABH4C)  ---AP144L
12UniProtVAR_021770G149RDHPR_HUMANDisease (HPABH4C)  ---AG148R
13UniProtVAR_006966Y150CDHPR_HUMANDisease (HPABH4C)104893866AY149C
14UniProtVAR_006967G151SDHPR_HUMANDisease (HPABH4C)  ---AG150S
15UniProtVAR_006968H158YDHPR_HUMANDisease (HPABH4C)750201480AH157Y
16UniProtVAR_006969G170SDHPR_HUMANDisease (HPABH4C)769460415AG169S
17UniProtVAR_006970F212CDHPR_HUMANDisease (HPABH4C)  ---AF211C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (17, 34)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_008121L14PDHPR_HUMANDisease (HPABH4C)756639609AL13P
02UniProtVAR_021767G17RDHPR_HUMANDisease (HPABH4C)757483045AG16R
03UniProtVAR_008122G17VDHPR_HUMANDisease (HPABH4C)  ---AG16V
04UniProtVAR_021768G18DDHPR_HUMANDisease (HPABH4C)  ---AG17D
05UniProtVAR_006960G23DDHPR_HUMANDisease (HPABH4C)104893863AG22D
06UniProtVAR_006961W36RDHPR_HUMANDisease (HPABH4C)104893865AW35R
07UniProtVAR_013027S51TDHPR_HUMANPolymorphism  ---AS50T
08UniProtVAR_021769Q66RDHPR_HUMANDisease (HPABH4C)  ---AQ65R
09UniProtVAR_006962L74PDHPR_HUMANDisease (HPABH4C)  ---AL73P
10UniProtVAR_006963W108GDHPR_HUMANDisease (HPABH4C)104893864AW107G
11UniProtVAR_006965P145LDHPR_HUMANDisease (HPABH4C)  ---AP144L
12UniProtVAR_021770G149RDHPR_HUMANDisease (HPABH4C)  ---AG148R
13UniProtVAR_006966Y150CDHPR_HUMANDisease (HPABH4C)104893866AY149C
14UniProtVAR_006967G151SDHPR_HUMANDisease (HPABH4C)  ---AG150S
15UniProtVAR_006968H158YDHPR_HUMANDisease (HPABH4C)750201480AH157Y
16UniProtVAR_006969G170SDHPR_HUMANDisease (HPABH4C)769460415AG169S
17UniProtVAR_006970F212CDHPR_HUMANDisease (HPABH4C)  ---AF211C

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.DHPR_HUMAN137-165  1A:136-164
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_SHORTPS00061 Short-chain dehydrogenases/reductases family signature.DHPR_HUMAN137-165  2A:136-164

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002812431aENSE00001693584chr4:17513857-17513573285DHPR_HUMAN1-35351A:8-3427
1.3ENST000002812433ENSE00001133183chr4:17510986-1751089493DHPR_HUMAN36-66311A:35-6531
1.4ENST000002812434ENSE00001133173chr4:17506098-1750600297DHPR_HUMAN67-99331A:66-9833
1.5ENST000002812435ENSE00001000268chr4:17503482-17503342141DHPR_HUMAN99-146481A:98-14548
1.6cENST000002812436cENSE00001133162chr4:17493963-17493855109DHPR_HUMAN146-182371A:145-18137
1.7aENST000002812437aENSE00001133153chr4:17492368-1749228584DHPR_HUMAN182-210291A:181-20929
1.8fENST000002812438fENSE00001000269chr4:17488859-17488021839DHPR_HUMAN210-244351A:209-24335

(-) Sequences/Alignments

Asymmetric 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:236
 aligned with DHPR_HUMAN | P09417 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:236
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      
           DHPR_HUMAN     9 EARRVLVYGGRGALGSRCVQAFRARNWWVASVDVVENEEASASIIVKMTDSFTEQADQVTAEVGKLLGEEKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPPGAAAIAVLPVTLDTPMNRKSMPEADFSSWTPLEFLVETFHDWITGKNRPSSGSLIQVVTTEGRTELTPAYF 244
               SCOP domains d1hdra_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                   SCOP domains
               CATH domains 1hdrA00 A:8-243 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..eeeeee....hhhhhhhhh......eeeeee........eeeee.....hhhhhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhh......hhhhhhhhhhhhhhhhhh..........------------hhhhhh-----hhh---hhhhhhhhhhhh.........eeeeeeee..eeeeeee.. Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeeeeeeeeeeee---------------------------------------- Sec.struct. author (2)
             SAPs(SNPs) (1) -----P--RD----D------------R--------------T--------------R-------P---------------------------------G------------------------------------L---RCS------Y-----------S-----------------------------------------C-------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------V----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:136-164    ------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:8-34     Exon 1.3  PDB: A:35-65         Exon 1.4  PDB: A:66-98           ----------------------------------------------Exon 1.6c  PDB: A:145-181            ---------------------------Exon 1.8f  PDB: A:209-243           Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.5  PDB: A:98-145 UniProt: 99-146         -----------------------------------Exon 1.7a  PDB: A:181-209    ---------------------------------- Transcript 1 (2)
                 1hdr A   8 EARRVLVYGGRGALGSRCVQAFRARNWWVASVDVVENEEASASIIVKMTDSFTEQADQVTAEVGKLLGEEKVDAILCVAGGWAGGNAKSKSLFKNCDLMWKQSIWTSTISSHLATKHLKEGGLLTLAGAKAALDGTPGMIGYGMAKGAVHQLCQSLAGKNSGMPPGAAAIAVLPVTLDTPMNRKSMPEADFSSWTPLEFLVETFHDWITGKNRPSSGSLIQVVTTEGRTELTPAYF 243
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237      

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HDR)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (DHPR_HUMAN | P09417)
molecular function
    GO:0004155    6,7-dihydropteridine reductase activity    Catalysis of the reaction: NADP+ + 5,6,7,8-tetrahydropteridine = NADPH + H+ + 6,7-dihydropteridine.
    GO:0070404    NADH binding    Interacting selectively and non-covalently with the reduced form, NADH, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006559    L-phenylalanine catabolic process    The chemical reactions and pathways resulting in the breakdown of phenylalanine, 2-amino-3-phenylpropanoic acid.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
    GO:0035690    cellular response to drug    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0051066    dihydrobiopterin metabolic process    The chemical reactions and pathways involving a dihydrobiopterin, a reduced pteridine derivative related to folic acid; it acts as an electron carrier in tyrosine biosynthesis and its quinoid form is produced by oxidation of tetrahydrobiopterin in several biological hydroxylation reactions.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0010044    response to aluminum ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aluminum ion stimulus.
    GO:0033762    response to glucagon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus.
    GO:0010288    response to lead ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
    GO:0006729    tetrahydrobiopterin biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.

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