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(-) Description

Title :  STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-((5-(3-AMINOPROPYL)-1,3-PHENYLENE)BIS( ETHANE-2,1-DIYL))BIS(4-METHYLPYRIDIN-2-AMINE)
 
Authors :  J. K. Holden, T. L. Poulos
Date :  22 Oct 14  (Deposition) - 14 Jan 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.02
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase, Nitric, Nitric Oxide Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Holden, S. Kang, S. A. Hollingsworth, H. Li, N. Lim, S. Chen, H. Huang, F. Xue, W. Tang, R. B. Silverman, T. L. Poulos
Structure-Based Design Of Bacterial Nitric Oxide Synthase Inhibitors.
J. Med. Chem. V. 58 994 2015
PubMed-ID: 25522110  |  Reference-DOI: 10.1021/JM501723P

(-) Compounds

Molecule 1 - NITRIC OXIDE SYNTHASE OXYGENASE
    Chains: A, B
    EC Number: 1.14.13.165
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: NOSOXY-LIKE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
112S2Ligand/Ion6,6'-{[5-(3-AMINOPROPYL)BENZENE-1,3-DIYL]DIETHANE-2,1-DIYL}BIS(4-METHYLPYRIDIN-2-AMINE)
2CL2Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:60 , ARG A:65 , CYS A:66 , PHE A:235 , ASN A:236 , GLY A:237 , TRP A:238 , GLU A:243 , TRP A:329 , TYR A:355 , TYR A:357 , 12S A:904 , HOH A:2231 , HOH A:2334 , HOH A:2367 , HOH A:2368BINDING SITE FOR RESIDUE HEM A 901
2AC2SOFTWAREGLN A:129 , ARG A:132 , TYR A:239 , ASN A:248BINDING SITE FOR RESIDUE CL A 903
3AC3SOFTWAREHIS A:128 , PHE A:235 , TRP A:238 , GLU A:243 , ARG A:247 , THR A:328 , TRP A:329 , TYR A:357 , HEM A:901 , HOH A:2137 , PHE B:342BINDING SITE FOR RESIDUE 12S A 904
4AC4SOFTWAREGLY A:159 , TRP A:160 , ARG A:161 , TRP A:238 , SER A:298 , ILE A:299 , GLN A:308 , HOH A:2300BINDING SITE FOR RESIDUE GOL A 905
5AC5SOFTWARETRP B:60 , ARG B:65 , CYS B:66 , PHE B:235 , ASN B:236 , GLY B:237 , TRP B:238 , GLU B:243 , TRP B:329 , TYR B:355 , TYR B:357 , 12S B:904 , HOH B:2329 , HOH B:2330BINDING SITE FOR RESIDUE HEM B 901
6AC6SOFTWAREGLN B:129 , ARG B:132 , TYR B:239 , ASN B:248 , HOH B:2143BINDING SITE FOR RESIDUE CL B 903
7AC7SOFTWAREPHE A:342 , HIS B:128 , PHE B:235 , TRP B:238 , GLU B:243 , ARG B:247 , THR B:328 , TRP B:329 , TYR B:357 , HEM B:901BINDING SITE FOR RESIDUE 12S B 904
8AC8SOFTWAREGLU B:156 , TRP B:160 , ARG B:161 , TRP B:238 , SER B:298 , ILE B:299 , HOH B:2168 , HOH B:2279 , HOH B:2286 , HOH B:2331BINDING SITE FOR RESIDUE GOL B 907
9AC9SOFTWAREGLU A:363 , TRP B:8 , LYS B:36 , ASP B:40BINDING SITE FOR RESIDUE PEG B 908

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D3K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:352 -Pro A:353
2Lys B:352 -Pro B:353

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4D3K)

(-) 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: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...eeee..eee....ee..eehhhhhh..........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh......hhhhhh...hhhhhhhhhh.........eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3k 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  


Chain B 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...eeee..eee....ee..eehhhhhh..........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh......hhhhhh...hhhhhhhhhh.........eee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d3k B   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)
  - → 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 4D3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D3K)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys A:352 - Pro A:353   [ RasMol ]  
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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 4d3m 4d3n 4d3o 4d3t 4d3u 4d3v 4d7h 4d7i 4d7j 4lwa 4lwb 4ug5 4ug6 4ug7 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

4d3i STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-((5-(AMINOMETHYL)-1,3-PHENYLENE) BIS(ETHANE-2,1-DIYL))BIS(4-METHYLPYRIDIN-2-AMINE)
4d3j STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6,6'-(2,2'-(5-AMINO-1,3-PHENYLENE) BIS(ETHANE-2,1-DIYL))BIS(4-METHYLPYRIDIN-2-AMINE)
4d3m STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 3-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL) ETHYL)-5-(2-(4-METHYL-6-(METHYLAMINO)PYRIDIN-2-YL) ETHYL)BENZONITRILE
4d3n STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 3-(2-(6-AMINO-4-METHYLPYRIDIN-2-YL) ETHYL)-5-((2-(PYRIDIN-2-YL)ETHYL)AMINO)BENZONITRILE
4d3o STRUCTURE OF BACILLUS SUBTILIS NITRIC OXIDE SYNTHASE IN COMPLEX WITH 6-(3-(2-(1H-PYRROLO(2,3-B)PYRIDIN- 6-YL)ETHYL)-5-(AMINOMETHYL)PHENETHYL)-4-METHYLPYRIDIN- 2-AMINE