Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NADPH-CYTOCHROME P450 REDUCTASE(A287P MUTANT)
 
Authors :  C. Xia, C. Marohnic, S. Panda, B. S. Masters, J. J. K. Kim
Date :  06 Nov 15  (Deposition) - 17 Aug 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Human Cypor, Abs-Like Phenotype, Flavoprotein, Cytochrome P450 Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Mccammon, S. P. Panda, C. Xia, J. J. Kim, D. Moutinho, M. Kranendonk, R. J. Auchus, E. M. Lafer, D. Ghosh, P. Martasek, R. Kar, B. S. Masters, L. J. Roman
Instability Of The Human Cytochrome P450 Reductase A287P Variant Is The Major Contributor To Its Antley-Bixler Syndrome-Like Phenotype.
J. Biol. Chem. V. 291 20487 2016
PubMed-ID: 27496950  |  Reference-DOI: 10.1074/JBC.M116.716019

(-) Compounds

Molecule 1 - NADPH--CYTOCHROME P450 REDUCTASE
    Chains: A, B
    EC Number: 1.6.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-CYPOR
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 57-677
    Gene: POR, CYPOR
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: P450R

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3NAP2Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:89 , GLN A:90 , THR A:91 , GLY A:92 , THR A:93 , ALA A:94 , ALA A:141 , THR A:142 , TYR A:143 , GLY A:146 , LEU A:176 , GLY A:177 , ASN A:178 , TYR A:181 , HIS A:183 , PHE A:184 , ASN A:185 , ASP A:211 , LEU A:215 , HOH A:855 , HOH A:871binding site for residue FMN A 701
2AC2SOFTWAREARG A:427 , ARG A:457 , TYR A:458 , TYR A:459 , SER A:460 , CYS A:475 , ALA A:476 , VAL A:477 , VAL A:479 , TYR A:481 , GLY A:491 , VAL A:492 , ALA A:493 , THR A:494 , TRP A:679 , HOH A:824 , HOH A:826 , HOH A:833 , HOH A:839 , HOH A:848 , HOH A:869 , HOH A:874binding site for residue FAD A 702
3AC3SOFTWAREARG A:301 , GLY A:537 , THR A:538 , CYS A:569 , SER A:599 , ARG A:600 , LYS A:605 , TYR A:607 , GLN A:609 , ASN A:637 , MET A:638 , ASP A:641 , HOH A:806 , HOH A:889binding site for residue NAP A 703
4AC4SOFTWARESER B:89 , GLN B:90 , THR B:91 , GLY B:92 , THR B:93 , ALA B:94 , ALA B:141 , THR B:142 , TYR B:143 , GLY B:144 , GLY B:146 , LEU B:176 , GLY B:177 , ASN B:178 , TYR B:181 , HIS B:183 , PHE B:184 , ASN B:185 , ASP B:211 , LEU B:215 , FAD B:702binding site for residue FMN B 701
5AC5SOFTWAREASN A:506 , GLY A:507 , GLY A:508 , ARG B:427 , ARG B:457 , TYR B:458 , TYR B:459 , SER B:460 , CYS B:475 , ALA B:476 , VAL B:477 , VAL B:479 , TYR B:481 , GLY B:491 , VAL B:492 , ALA B:493 , THR B:494 , THR B:538 , TRP B:679 , FMN B:701 , HOH B:804 , HOH B:808 , HOH B:815 , HOH B:823 , HOH B:838 , HOH B:862binding site for residue FAD B 702
6AC6SOFTWAREARG B:301 , GLY B:537 , THR B:538 , CYS B:569 , SER B:599 , ARG B:600 , LYS B:605 , TYR B:607 , GLN B:609 , MET B:638 , ASP B:641binding site for residue NAP B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EMN)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:277 -Pro A:278
2Cys A:366 -Pro A:367
3Pro B:277 -Pro B:278
4Cys B:366 -Pro B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EMN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EMN)

(-) Exons   (0, 0)

(no "Exon" information available for 5EMN)

(-) 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:607
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh...eeeeeeeee...ee...hhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhh..eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh........eeeee....hhhhh..........................eeeeeee........eeeeeee............eeee....hhhhhhhhhhhh......eeeeee..............eehhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhh......hhhhhhhhh.....eeee..........eeeeeee..eee.....eeehhhhhhhhh..............eeee.............eeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emn A  70 SSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDNALVVFCMATYGEGDPTDNAQDFYDWLQETDVDLSGVKFAVFGLGNKTYEHFNAMGKYVDKRLEQLGAQRIFELGLGDDDGNLEEDFITWREQFWLAVCEHFGVEATGIRQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLPAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPVGENGGRALVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS 680
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239||     253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       
                                                                                                                                                                                                    240|                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                                                                                                                                                                                                     245                                                                                                                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:597
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh...eeeeeeeee...ee...hhhhhhhhhhh.......eeeeeeee.......hhhhhhhhhhhhhh..ee....eeee...hhhhhhhhhhhhhhhhhhhhhh......eeeee....hhhhh..........................eeeeeee........eeeeeee............eeee....hhhhhhhhhhhhh.....eeeeee..............eehhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhh......hhhhhhhhh.....eeee..........eeeeeee..eee.....eeehhhhhhhhh......eeee.............eeee.hhhhhhhhhhhhhhhhhhhhh......eeeeeee........hhhhhhhhhhh....eeeeee........hhhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emn B  70 SSFVEKMKKTGRNIIVFYGSQTGTAEEFANRLSKDAHRYGMRGMSADPEEYDLADLSSLPEIDNALVVFCMATYGEGDPTDNAQDFYDWLQETDVDLSGVKFAVFGLGNKTYEHFNAMGKYVDKRLEQLGAQRIFELGLGDDDGNLEEDFITWREQFWLAVCEHFGVEAIRQYELVVHTDIDAAKVYMGEMGRLKSYENQKPPFDAKNPFLPAVTTNRKLNQGTERHLMHLELDISDSKIRYESGDHVAVYPANDSALVNQLGKILGADLDVVMSLNNLDEESNKKHPFPCPTSYRTALTYYLDITNPPRTNVLYELAQYASEPSEQELLRKMASSSGEGKELYLSWVVEARRHILAILQDCPSLRPPIDHLCELLPRLQARYYSIASSSKVHPNSVHICAVVVEYETKAGRINKGVATNWLRAKEPLVPMFVRKSQFRLPFKATTPVIMVGPGTGVAPFIGFIQERAWLRQQGKEVGETLLYYGCRRSDEDYLYREELAQFHRDGALTQLNVAFSREQSHKVYVQHLLKQDREHLWKLIEGGAHIYVCGDARNMARDVQNTFYDIVAELGAMEHAQAVDYIKKLMTKGRYSLDVWS 680
                                    79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495      |513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       
                                                                                                                                                                                                  238|                                                                                                                                                                                                                                                              502|                                                                                                                                                                         
                                                                                                                                                                                                   245                                                                                                                                                                                                                                                               511
   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 5EMN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EMN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EMN)

(-) Gene Ontology  (44, 44)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:366 - Pro A:367   [ RasMol ]  
    Cys B:366 - Pro B:367   [ RasMol ]  
    Pro A:277 - Pro A:278   [ RasMol ]  
    Pro B:277 - Pro B:278   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5emn
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  NCPR_HUMAN | P16435
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.6.2.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  NCPR_HUMAN | P16435
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NCPR_HUMAN | P16435: 1b1c 3fjo 3qe2 3qfc 3qfr 3qfs 3qft 5fa6

(-) Related Entries Specified in the PDB File

3qe2 3QE2 IS THE WILD TYPE FORM