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(-) Description

Title :  STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 3,5-BIS(2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL) BENZONITRILE
 
Authors :  J. K. Holden, T. L. Poulos
Date :  22 Mar 15  (Deposition) - 24 Jun 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nitric Oxide Synthase, Oxidoreductase, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Holden, D. Dejam, M. C. Lewis, H. Huang, S. Kang, Q. Jing, F. Xue, R. B. Silverman, T. L. Poulos
Inhibitor Bound Crystal Structures Of Bacterial Nitric Oxide Synthase.
Biochemistry V. 54 4075 2015
PubMed-ID: 26062720  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00431

(-) Compounds

Molecule 1 - NITRIC OXIDE SYNTHASE OXYGENASE
    Atcc: ATCC 23857
    Chains: A
    EC Number: 1.14.13.165
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: NOSOXY-LIKE PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
11EV1Ligand/Ion3,5-BIS[2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL]BENZONITRILE
2CL1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4H4B1Ligand/Ion5,6,7,8-TETRAHYDROBIOPTERIN
5HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
11EV2Ligand/Ion3,5-BIS[2-(6-AMINO-4-METHYLPYRIDIN-2-YL)ETHYL]BENZONITRILE
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4H4B2Ligand/Ion5,6,7,8-TETRAHYDROBIOPTERIN
5HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:60 , CYS A:66 , PHE A:235 , ASN A:236 , GLY A:237 , TRP A:238 , GLU A:243 , TYR A:355 , H4B A:902 , 1EV A:904 , HOH A:2181 , HOH A:2287 , HOH A:2289BINDING SITE FOR RESIDUE HEM A 901
2AC2SOFTWAREARG A:247 , TRP A:327 , THR A:328 , TRP A:329 , PHE A:342 , HIS A:343 , ARG A:344 , HEM A:901 , HOH A:2194 , HOH A:2267BINDING SITE FOR RESIDUE H4B A 902
3AC3SOFTWAREGLN A:129 , TYR A:239 , ASN A:248 , 1EV A:904 , HOH A:2190BINDING SITE FOR RESIDUE CL A 903
4AC4SOFTWAREARG A:65 , ARG A:132 , ILE A:218 , PHE A:235 , TRP A:238 , TYR A:239 , GLU A:243 , ASN A:248 , ARG A:254 , TRP A:329 , TYR A:357 , HEM A:901 , CL A:903BINDING SITE FOR RESIDUE 1EV A 904
5AC5SOFTWAREGLU A:156 , TRP A:160 , ARG A:161 , TRP A:238 , SER A:298 , ILE A:299 , HOH A:2128 , HOH A:2240 , HOH A:2241 , HOH A:2249BINDING SITE FOR RESIDUE GOL A 905
6AC6SOFTWAREVAL A:183 , TRP A:184 , TYR A:271 , ASN A:272 , HOH A:2148 , HOH A:2216 , HOH A:2290BINDING SITE FOR RESIDUE GOL A 906
7AC7SOFTWAREARG A:142 , ASP A:166 , ARG A:254 , TYR A:255 , LYS A:257 , HOH A:2114 , HOH A:2203BINDING SITE FOR RESIDUE GOL A 907

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4UG7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:352 -Pro A:353

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4UG7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UG7)

(-) Exons   (0, 0)

(no "Exon" information available for 4UG7)

(-) 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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.....hhhhhhhheeee.....hhhhhhhhhhhhhhhhhhhhh...eeee..........eee.........eeee..eeee...hhhhhhhhhhh.............eeeee......eee..hhhhh.eee.....hhhhhhhh.eee...ee..eeeee..eee....ee..eehhhhhh..........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhh.........eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ug7 A   2 EEKEILWNEAKAFIAACYQELGKAAEVKDRLADIKSEIDLTGSYVHTKEELEHGAKMAWRNSNRCIGRLFWNSLNVIDRRDVRTKEEVRDALFHHIETATNNGKIRPTITIFPPEEKGEKQVEIWNHQLIRYAGYESDGERIGDPASCSLTAACEELGWRGERTDFDLLPLIFRMKGDEQPVWYELPRSLVIEVPITHPDIEAFSDLELKWYGVPIISDMKLEVGGIHYNAAPFNGWYMGTEIGARNLADEKRYDKLKKVASVIGIAADYNTDLWKDQALVELNKAVLHSYKKQGVSIVDHHTAASQFKRFEEQAEEAGRKLTGDWTWLIPPISPAATHIFHRSYDNSIVKPNYFYQDKPYE 363
                                    11        21        31        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       311       321       331       341       351       361
   Legend:   → Mismatch (orange background)
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  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 4UG7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4UG7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4UG7)

(-) Gene Ontology  (7, 7)

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    Lys A:352 - Pro A:353   [ RasMol ]  
 
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  4ug7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
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  NOSO_BACSU | O34453
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  1.14.13.165
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 Related Entries

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

UniProtKB/Swiss-Prot
        NOSO_BACSU | O34453: 1m7v 1m7z 2amo 2an0 2an2 2fbz 2fc1 2fc2 4d3i 4d3j 4d3k 4d3m 4d3n 4d3o 4d3t 4d3u 4d3v 4d7h 4d7i 4d7j 4lwa 4lwb 4ug5 4ug6 4ug8 4ug9 4uga 4ugb 4ugc 4ugd 4uge 4ugf 4ugg 4ugh 4ugi 4ugj 4ugk 4ugl 4ugm 4ugn 4ugo 4ugp 4ugq 4ugr 4ugs 4ugt 4ugu 4ugv 4ugw 4ugx 4ugy 4uqr 4uqs 5g65 5g66 5g67 5g68 5g69 5g6a 5g6b 5g6c 5g6d 5g6e 5g6f 5g6g 5g6h 5g6i 5g6j 5g6k 5g6l 5g6m 5g6n 5g6o 5g6p 5g6q

(-) Related Entries Specified in the PDB File

4ug5 STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(2-(5-(2-(2-AMINO-6-METHYLPYRIDIN- 4-YL)ETHYL)PYRIDIN-3-YL)ETHYL)-4-METHYLPYRIDIN-2- AMINE
4ug6 STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-(PYRIDINE-3,5-DIYLDIETHANE-2,1- DIYL)BIS(4-METHYLPYRIDIN-2-AMINE)
4ug8 STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(5-((3R,4R)-4-((6-AZANYL-4-METHYL -PYRIDIN-2-YL)METHYL)PYRROLIDIN-3-YL)OXYPENTYL)-4- METHYL-PYRIDIN-2-AMINE
4ug9 STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-((4-(3-AMINOPROPYL)BENZENE-1,3- DIYL)DIETHANE-2,1-DIYL)BIS(4-METHYLPYRIDIN-2-AMINE)
4uga STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-((3-(((2-(3-FLUOROPHENYL)ETHYL)AMINO )METHYL)PHENOXY)METHYL)-4-METHYLPYRIDIN-2-AMINE
4ugb STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(((5-(((2-(3-FLUOROPHENYL)ETHYL)AMINO )METHYL)PYRIDIN-3-YL)OXY)METHYL)-4-METHYLPYRIDIN-2- AMINE
4ugc STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-(((2S)-3-AMINOPROPANE-1,2-DIYL) BIS(OXYMETHANEDIYL))BIS(4-METHYLPYRIDIN-2-AMINE)
4ugd STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-((((2S)-1-AMINO-4-((6-AMINO-4- METHYLPYRIDIN-2-YL)METHOXY)BUTAN-2-YL)OXY)METHYL)-4 -METHYLPYRIDIN-2-AMINE
4uge STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 4-METHYL-6-((3-(PIPERIDIN-4-YLMETHOXY) PHENOXY)METHYL)PYRIDIN-2-AMINE
4ugf STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-((((3S, 5R)-5-(((6-AMINO-4- METHYLPYRIDIN-2-YL)METHOXY)METHYL)PYRROLIDIN-3-YL)OXY )METHYL)-4-METHYLPYRIDIN-2-AMINE
4ugg STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH (R)-6-(2-AMINO-2-(3-(2-(6-AMINO-4 -METHYLPYRIDIN-2-YL)ETHYL)PHENYL)ETHYL)-4-METHYLPYRIDIN -2-AMINE
4ugh STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N1-(3-(2-(6-AMINO-4-METHYLPYRIDIN-2- YL)ETHYL)PHENYL)-N1,N2-DIMETHYLETHANE-1,2-DIAMINE
4ugi STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N1-(6-(2-(6-AMINO-4-METHYLPYRIDIN-2- YL)ETHYL)PYRIDIN-2-YL)-N1,N2-DIMETHYLETHANE-1,2- DIAMINE
4ugj STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 3-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL) ETHYL)-5-(METHYL(2-(METHYLAMINO)ETHYL)AMINO)BENZONITRILE
4ugk STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(2-(5-(2-(DIMETHYLAMINO)ETHYL)PYRIDIN -3-YL)ETHYL)-4-METHYLPYRIDIN-2-AMINE
4ugl STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N1-(3-(2-(6-AMINO-4-METHYLPYRIDIN-2- YL)ETHYL)-5-FLUOROPHENYL)-N1-CYCLOPROPYL-N2-METHYLETHANE -1,2-DIAMINE
4ugm STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N,N'-(ETHANE-1,2-DIYLDIBENZENE-3,1- DIYL)DITHIOPHENE-2-CARBOXIMIDAMIDE
4ugn STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH (S)-N-(3-(((PYRROLIDIN-2-YLMETHYL)AMINO )METHYL)PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE
4ugo STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N-(4-(2-(ETHYL(3-(((E)-IMINO(THIOPHEN -2-YL)METHYL)AMINO)BENZYL)AMINO)ETHYL)PHENYL) THIOPHENE-2-CARBOXIMIDAMIDE
4ugp STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N',N'-(((2R)-3-AMINOPROPANE-1,2-DIYL )BIS(OXYMETHANEDIYLBENZENE-3,1-DIYL))DITHIOPHENE-2- CARBOXIMIDAMIDE
4ugq STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N,N''-(((2S)-3-AMINOPROPANE-1,2-DIYL )BIS(OXYMETHANEDIYLBENZENE-3,1-DIYL))DITHIOPHENE-2- CARBOXIMIDAMIDE
4ugr STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N-(3-(((2S,4S)-4-((3-((C-THIOPHEN-2 -YLCARBONIMIDOYL)AMINO)PHENYL)METHOXY)PYRROLIDIN-2-YL) METHOXYMETHYL)PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE
4ugs STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N,N'-(ETHANE-1,2-DIYLBIS(OXYBENZENE-3 ,1-DIYL))DITHIOPHENE-2-CARBOXIMIDAMIDE
4ugt STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N-(3-((PYRROLIDIN-3-YLOXY)METHYL)PHENYL )THIOPHENE-2-CARBOXIMIDAMIDE
4ugu STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N'-(4-(((2S,4R)-4-(3-((C-THIOPHEN-2 -YLCARBONIMIDOYL)AMINO)PHENOXY)PYRROLIDIN-2-YL)METHOXY) PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE
4ugv STRUCTURE OF Y357F BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH ARGININE AND 5,6,7,8- TETRAHYDROBIOPTERIN
4ugw STRUCTURE OF Y357F BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(5-((3R,4R)-4-((6- AZANYL-4-METHYL-PYRIDIN-2-YL)METHYL)PYRROLIDIN-3-YL )OXYPENTYL)-4-METHYL-PYRIDIN-2-AMINE
4ugx STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N-(3-((ETHYL(2-(3-FLUOROPHENYL)ETHYL) AMINO)METHYL)PHENYL)THIOPHENE-2-CARBOXIMIDAMIDE
4ugy STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH N1-(5-(2-(6-AMINO-4-METHYLPYRIDIN-2- YL)ETHYL)PYRIDIN-3-YL)-N1,N2-DIMETHYLETHANE-1,2- DIAMINE