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

(-) Description

Title :  STRUCTURE OF BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN IN COMPLEX WITH N-(3-(((3-FLUOROPHENETHYL)AMINO)METHYL)PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE
 
Authors :  H. Li, T. L. Poulos
Date :  24 Apr 13  (Deposition) - 12 Feb 14  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitric Oxide Synthase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Huang, H. Li, S. Yang, G. Chreifi, P. Martasek, L. J. Roman, F. L. Meyskens, T. L. Poulos, R. B. Silverman
Potent And Selective Double-Headed Thiophene-2-Carboximidamide Inhibitors Of Neuronal Nitric Oxide Synthase For The Treatment Of Melanoma.
J. Med. Chem. V. 57 686 2014
PubMed-ID: 24447275  |  Reference-DOI: 10.1021/JM401252E

(-) Compounds

Molecule 1 - NITRIC OXIDE SYNTHASE, ENDOTHELIAL
    Chains: A, B
    EC Number: 1.14.13.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCWORI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HEME DOMAIN (UNP RESIDUES 40-482)
    Gene: NOS3
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: CONSTITUTIVE NOS, CNOS, EC-NOS, ENDOTHELIAL NOS, ENOS, NOS TYPE III, NOSIII

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
15H32Ligand/IonN-[3-({[2-(3-FLUOROPHENYL)ETHYL]AMINO}METHYL)PHENYL]THIOPHENE-2-CARBOXIMIDAMIDE
2ACT4Ligand/IonACETATE ION
3CAS2Mod. Amino AcidS-(DIMETHYLARSENIC)CYSTEINE
4GOL2Ligand/IonGLYCEROL
5H4B2Ligand/Ion5,6,7,8-TETRAHYDROBIOPTERIN
6HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
7ZN1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:180 , ARG A:185 , CYS A:186 , SER A:228 , PHE A:355 , SER A:356 , TRP A:358 , GLU A:363 , TRP A:449 , PHE A:475 , TYR A:477 , H4B A:502 , 5H3 A:503 , HOH A:622 , HOH A:662 , HOH A:725BINDING SITE FOR RESIDUE HEM A 501
02AC2SOFTWARESER A:104 , VAL A:106 , ARG A:367 , ALA A:448 , TRP A:449 , HEM A:501 , GOL A:506 , HOH A:603 , HOH A:622 , HOH A:647 , HOH A:692 , TRP B:447 , PHE B:462 , HIS B:463 , GLN B:464 , GLU B:465BINDING SITE FOR RESIDUE H4B A 502
03AC3SOFTWAREVAL A:106 , LEU A:107 , PRO A:336 , VAL A:338 , PHE A:355 , SER A:356 , GLY A:357 , TRP A:358 , GLU A:363 , HEM A:501 , HOH A:725BINDING SITE FOR RESIDUE 5H3 A 503
04AC4SOFTWARETRP A:358 , VAL A:420 , SER A:428 , HOH A:762BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREGLN A:249 , ARG A:252 , ASN A:368 , ARG A:374 , HOH A:617 , HOH A:708BINDING SITE FOR RESIDUE ACT A 505
06AC6SOFTWAREVAL A:106 , ARG A:367 , HIS A:373 , TRP A:449 , H4B A:502 , HOH A:603 , TRP B:76BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWARECYS A:96 , CYS A:101 , CYS B:96 , CYS B:101BINDING SITE FOR RESIDUE ZN A 507
08AC8SOFTWARETRP B:180 , ARG B:185 , CYS B:186 , VAL B:187 , SER B:228 , PHE B:355 , SER B:356 , TRP B:358 , GLU B:363 , TRP B:449 , TYR B:477 , H4B B:502 , 5H3 B:503 , HOH B:629 , HOH B:686 , HOH B:723BINDING SITE FOR RESIDUE HEM B 501
09AC9SOFTWARETRP A:447 , PHE A:462 , GLU A:465 , HOH A:606 , SER B:104 , ARG B:367 , ALA B:448 , TRP B:449 , HEM B:501 , GOL B:506 , HOH B:629 , HOH B:659 , HOH B:685BINDING SITE FOR RESIDUE H4B B 502
10BC1SOFTWARETRP A:76 , LEU B:107 , PRO B:336 , VAL B:338 , PHE B:355 , SER B:356 , GLY B:357 , TRP B:358 , GLU B:363 , HEM B:501 , GOL B:506BINDING SITE FOR RESIDUE 5H3 B 503
11BC2SOFTWARETRP B:358 , VAL B:420 , SER B:428 , HOH B:760 , HOH B:761 , HOH B:762 , HOH B:766BINDING SITE FOR RESIDUE ACT B 504
12BC3SOFTWAREGLN B:249 , ARG B:252 , ASN B:368 , ARG B:374 , HOH B:634BINDING SITE FOR RESIDUE ACT B 505
13BC4SOFTWAREHOH A:606 , VAL B:106 , ARG B:367 , HIS B:373 , TRP B:449 , H4B B:502 , 5H3 B:503BINDING SITE FOR RESIDUE GOL B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4KCR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:472 -Pro A:473
2Ser B:472 -Pro B:473

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KCR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KCR)

(-) Exons   (0, 0)

(no "Exon" information available for 4KCR)

(-) 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:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4kcra_ A: Nitric oxide (NO) synthase oxygenase domain                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eee.hhhhhh....................hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh...eeee...........ee.........eee.....eee...hhhhhhhhhhh.............eeee......eee..hhhhh.eee.....hhhhhhhh.eee...ee...eeee..eee....ee...hhhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhh.........eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kcr A  67 GPKFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCSSAQEMFTYICNHIKYATNRGNLRSAITVFPQRAPGRGDFRIWNSQLVRYAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEAPELFVLPPELVLEVPLEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEFSAAPFSGWYMSTEIGTRNLCDPHRYNILEDVAVcMDLDTRTTSSLWKDKAAVEINLAVLHSFQLAKVTIVDHHAATVSFMKHLDNEQKARGGCPADWAWIVPPISGSLTPVFHQEMVNYILSPAFRYQPDPW 482
                                    76        86        96       106  ||   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377      |387       397       407       417       427       437       447       457       467       477     
                                                                    109|                                                                                                                                                                                                                                                                    384-CAS                                                                                              
                                                                     121                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:403
                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4kcrb_ B: Nitric oxide (NO) synthase oxygenase domain                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee......eee.hhhhhh....................hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhh...eeee...........ee.........eee.....eee...hhhhhhhhhhh.............eeee......eee..hhhhh.eee.....hhhhhhhh.eee...ee...eeee..eee....ee..eehhhhhhhhhhh.....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhh.........eee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kcr B  69 KFPRVKNWELGSITYDTLCAQSQQDGPCTPRRCLGSLVLPRPAEQLLSQARDFINQYYSSIKRSGSQAHEERLQEVEAEVASTGTYHLRESELVFGAKQAWRNAPRCVGRIQWGKLQVFDARDCSSAQEMFTYICNHIKYATNRGNLRSAITVFPQRAPGRGDFRIWNSQLVRYAGYRQQDGSVRGDPANVEITELCIQHGWTPGNGRFDVLPLLLQAPDEAPELFVLPPELVLEVPLEHPTLEWFAALGLRWYALPAVSNMLLEIGGLEFSAAPFSGWYMSTEIGTRNLCDPHRYNILEDVAVcMDLDTRTTSSLWKDKAAVEINLAVLHSFQLAKVTIVDHHAATVSFMKHLDNEQKARGGCPADWAWIVPPISGSLTPVFHQEMVNYILSPAFRYQPDPW 482
                                    78        88        98       108||     129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379    |  389       399       409       419       429       439       449       459       469       479   
                                                                  109|                                                                                                                                                                                                                                                                    384-CAS                                                                                              
                                                                   121
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KCR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KCR)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    5H3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CAS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H4B  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:472 - Pro A:473   [ RasMol ]  
    Ser B:472 - Pro B:473   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4kcr
    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
  NOS3_BOVIN | P29473
    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)
  1.14.13.39
    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
  NOS3_BOVIN | P29473
    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
        NOS3_BOVIN | P29473: 1d0c 1d0o 1d1v 1d1w 1d1x 1d1y 1dm6 1dm7 1dm8 1dmi 1dmj 1dmk 1ed4 1ed5 1ed6 1foi 1foj 1fol 1foo 1fop 1i83 1nse 1p6l 1p6m 1p6n 1q2o 1rs8 1rs9 1zzs 1zzt 2g6o 2hx2 2nse 3dqs 3dqt 3e7s 3jww 3jwx 3jwy 3jwz 3n5p 3n5q 3n5r 3n5s 3n5t 3nld 3nle 3nlf 3nlg 3nlh 3nli 3nlt 3nlu 3nse 3pnh 3rqo 3rqp 4c3a 4car 4cft 4cty 4ctz 4cu0 4cu1 4cul 4cum 4cun 4cvg 4cwv 4cww 4cwx 4cwy 4cwz 4cx0 4cx1 4cx2 4d33 4d34 4d35 4d36 4d37 4d38 4d39 4d3a 4imx 4jsk 4jsl 4jsm 4k5h 4k5i 4k5j 4k5k 4kcp 4kcq 4kcs 4luw 4nse 4uh7 4uh8 4uh9 4uha 4upq 4upr 4ups 4upt 5adj 5adk 5adl 5adm 5adn 5fj2 5fj3 5fvy 5fvz 5nse 5uod 6nse 7nse 8nse 9nse

(-) Related Entries Specified in the PDB File

4kch 4kci 4kcj 4kck 4kcl 4kcm 4kcn 4kco 4kcp 4kcq 4kcs