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(-) Description

Title :  STRUCTRUE OF S127P MUTANT OF CYTOCHROME B5 REDUCTASE
 
Authors :  M. C. Bewley, C. A. Davis, C. C. Marohnic, D. Taormina, M. J. Barber
Date :  04 Sep 03  (Deposition) - 14 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methemoglobinemia, Flavin Flexibility, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. C. Bewley, C. A. Davis, C. C. Marohnic, D. Taormina, M. J. Barber
The Structure Of The S127P Mutant Of Cytochrome B5 Reductase That Causes Methemoglobinemia Shows The Amp Moiety Of The Flavin Occupying The Substrate Binding Site
Biochemistry V. 42 13145 2003
PubMed-ID: 14609324  |  Reference-DOI: 10.1021/BI034915C
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NADH-CYTOCHROME B5 REDUCTASE
    ChainsA, B
    EC Number1.6.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21-CODON-PLUS (DE3)RIL
    Expression System Taxid562
    GeneDIA1
    MutationYES
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:77 , PRO B:92 , TYR B:93 , THR B:94 , VAL B:108 , VAL B:109 , LYS B:110 , TYR B:112 , GLY B:179 , GLY B:180 , THR B:181 , GLY B:182 , THR B:184 , ALA B:208 , ASN B:209 , GLN B:210 , ASP B:239 , PHE B:251 , GLY B:274 , PRO B:275 , PRO B:277 , MET B:278 , PHE B:300 , HOH B:310 , HOH B:321 , HOH B:330 , HOH B:346 , HOH B:365 , HOH B:371 , HOH B:375 , HOH B:389 , HOH B:411BINDING SITE FOR RESIDUE FAD B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QX4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:143 -Pro A:144
2Gly B:143 -Pro B:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QX4)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.NB5R3_RAT40-152
 
  2A:39-151
B:39-151

(-) Exons   (0, 0)

(no "Exon" information available for 1QX4)

(-) 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:264
 aligned with NB5R3_RAT | P20070 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:270
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
            NB5R3_RAT    32 PAITLENPDIKYPLRLIDKEIISHDTRRFRFALPSPQHILGLPIGQHIYLSTRIDGNLVIRPYTPVSSDDDKGFVDLVVKVYFKDTHPKFPAGGKMSQYLENMNIGDTIEFRGPNGLLVYQGKGKFAIRADKKSNPVVRTVKSVGMIAGGTGITPMLQVIRAVLKDPNDHTVCYLLFANQSEKDILLRPELEELRNEHSSRFKLWYTVDKAPDAWDYSQGFVNEEMIRDHLPPPGEETLILMCGPPPMIQFACLPNLERVGHPKERCFTF 301
               SCOP domains --d1qx4a1 A:33-153 cytochrome b5 reductase                                                                                 d1qx4a2 A:154-300 cytochrome b5 reductase                                                                                                           SCOP domains
               CATH domains ---------1qx4A01 A:40-145 Translation factors                                                                      1qx4A02 A:146-300 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........eeeeeeeeee....eeeeeee.....ee.......eeeeeeee..eeeeeee..........eeeeeee.....------..hhhhhhhhh.....eeeeeeee..eeeee..eeee........eeee..eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeee.hhh.hhhhhhhhhhhh...eeeeeeeee.......ee...hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------FAD_FR  PDB: A:39-151 UniProt: 40-152                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qx4 A  31 HMITLENPDIKYPLRLIDKEILSHDTRRFRFALPSPQHILGLPIGQHIYLSTRIDGNLVIRPYTPVSSDDDKGFVDLVVKVYFKE------AGGKMPQYLENMNIGDTIEFRGPNGLLVYQGKGKFAIRADKKSNPVVRTVKSVGMIAGGTGITPMLQVIRAVLKDPNDHTVCYLLFANQSEKDILLRPELEELRNEHSSRFKLWYTVDKAPDAWDYSQGFVNEEMIRDHLPPPGEETLILMCGPPPMIQFACLPNLERVGHPKERCFTF 300
                                    40        50        60        70        80        90       100       110    |    - |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
                                                                                                              115    122                                                                                                                                                                                  

Chain B from PDB  Type:PROTEIN  Length:264
 aligned with NB5R3_RAT | P20070 from UniProtKB/Swiss-Prot  Length:301

    Alignment length:270
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
            NB5R3_RAT    32 PAITLENPDIKYPLRLIDKEIISHDTRRFRFALPSPQHILGLPIGQHIYLSTRIDGNLVIRPYTPVSSDDDKGFVDLVVKVYFKDTHPKFPAGGKMSQYLENMNIGDTIEFRGPNGLLVYQGKGKFAIRADKKSNPVVRTVKSVGMIAGGTGITPMLQVIRAVLKDPNDHTVCYLLFANQSEKDILLRPELEELRNEHSSRFKLWYTVDKAPDAWDYSQGFVNEEMIRDHLPPPGEETLILMCGPPPMIQFACLPNLERVGHPKERCFTF 301
               SCOP domains --d1qx4b1 B:33-153 cytochrome b5 reductase                                                                                 d1qx4b2 B:154-300 cytochrome b5 reductase                                                                                                           SCOP domains
               CATH domains ---------1qx4B01 B:40-145 Translation factors                                                                      1qx4B02 B:146-300 Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........eeeeeeeeee....eeeeeee.....ee.......eeeeeeee..eeeeeee..........eeeeeee.....------..hhhhhhhhh.....eeeeeeee..eeeee..eeee........eeee..eeeeeee..hhhhhhhhhhhhhhh.....eeeeeeeeee.hhh.hhhhhhhhhhhh...eeeeeeeee.......ee...hhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhh.hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------FAD_FR  PDB: B:39-151 UniProt: 40-152                                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qx4 B  31 HMITLENPDIKYPLRLIDKEILSHDTRRFRFALPSPQHILGLPIGQHIYLSTRIDGNLVIRPYTPVSSDDDKGFVDLVVKVYFKE------AGGKMPQYLENMNIGDTIEFRGPNGLLVYQGKGKFAIRADKKSNPVVRTVKSVGMIAGGTGITPMLQVIRAVLKDPNDHTVCYLLFANQSEKDILLRPELEELRNEHSSRFKLWYTVDKAPDAWDYSQGFVNEEMIRDHLPPPGEETLILMCGPPPMIQFACLPNLERVGHPKERCFTF 300
                                    40        50        60        70        80        90       100       110    |    - |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
                                                                                                              115    122                                                                                                                                                                                  

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QX4)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NB5R3_RAT | P20070)
molecular function
    GO:0043531    ADP binding    Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
    GO:0016208    AMP binding    Interacting selectively and non-covalently with AMP, adenosine monophosphate.
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004128    cytochrome-b5 reductase activity, acting on NAD(P)H    Catalysis of the reaction: NAD(P)H + H+ + 2 ferricytochrome b(5) = NAD(P)+ + 2 ferrocytochrome b(5).
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0005811    lipid droplet    An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NB5R3_RAT | P200701i7p 1ib0

(-) Related Entries Specified in the PDB File

1i7p STRUCTURE OF CYTOCHROME B5 REDUCTASE COMPLEXED WITH NAD
1ib0 STRUCTURE OF CYTOCHROME B5 REDUCTASE FROM RAT