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(-) Description

Title :  SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH MACROLIDE INHIBITOR 29
 
Authors :  N. Maita, A. Sugawara, T. Sunazuka
Date :  30 Mar 15  (Deposition) - 01 Jul 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Chitinase, Inhibitor, Macrolide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Sugawara, N. Maita, H. Gouda, T. Yamamoto, T. Hirose, S. Kimura, Y. Saito, H. Nakano, T. Kasai, H. Nakano, K. Shiomi, S. Hirono, T. Watanabe, H. Taniguchi, S. Omura, T. Sunazuka
Creation Of Customized Bioactivity Within A 14-Membered Macrolide Scaffold: Design, Synthesis, And Biological Evaluation Using A Family-18 Chitinase
J. Med. Chem. V. 58 4984 2015
PubMed-ID: 26030312  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00175

(-) Compounds

Molecule 1 - CHITINASE B
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI DH5ALPHA
    Expression System Plasmid: PTRCHISB
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 668369
    Expression System Vector Type: PLASMID
    Gene: CHIB
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3M6A1Ligand/Ion(1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ETHYL-2,10-DIHYDROXY-2,6,8,10,12,15,15,17-OCTAMETHYL-5-OXO-9-(PROP-2-YN-1-YLOXY)-4,14,16-TRIOXABICYCLO[11.3.1]HEPTADEC-7-YL {2-[N'-(METHYLCARBAMOYL)CARBAMIMIDAMIDO]ETHYL}CARBAMATE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3M6A1Ligand/Ion(1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ETHYL-2,10-DIHYDROXY-2,6,8,10,12,15,15,17-OCTAMETHYL-5-OXO-9-(PROP-2-YN-1-YLOXY)-4,14,16-TRIOXABICYCLO[11.3.1]HEPTADEC-7-YL {2-[N'-(METHYLCARBAMOYL)CARBAMIMIDAMIDO]ETHYL}CARBAMATE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL12Ligand/IonGLYCEROL
3M6A2Ligand/Ion(1R,2R,3R,6R,7S,8S,9R,10R,12R,13S,17S)-3-ETHYL-2,10-DIHYDROXY-2,6,8,10,12,15,15,17-OCTAMETHYL-5-OXO-9-(PROP-2-YN-1-YLOXY)-4,14,16-TRIOXABICYCLO[11.3.1]HEPTADEC-7-YL {2-[N'-(METHYLCARBAMOYL)CARBAMIMIDAMIDO]ETHYL}CARBAMATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:10 , PHE A:12 , PHE A:51 , GLY A:96 , TRP A:97 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , TYR A:292 , ASP A:316 , ILE A:339 , TRP A:403 , HOH A:716 , HOH A:803binding site for residue M6A A 501
2AC2SOFTWAREPHE A:12 , ILE A:13 , PRO A:14 , THR A:15 , PHE A:51 , TYR A:99binding site for residue GOL A 502
3AC3SOFTWAREPRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:646 , HOH A:702binding site for residue GOL A 503
4AC4SOFTWAREARG A:244 , TRP A:252 , PHE A:259 , PRO A:260 , SER A:261binding site for residue GOL A 504
5AC5SOFTWAREARG A:4 , HIS A:46 , ARG A:89 , HOH A:640 , HOH A:664binding site for residue GOL A 505
6AC6SOFTWAREARG A:162 , ALA A:204 , ASP A:207 , LYS A:284 , HOH A:691binding site for residue GOL A 506
7AC7SOFTWARETYR A:323 , LEU A:325 , VAL A:326 , GLY A:327 , CYS A:328 , ASP A:329binding site for residue GOL A 507
8AC8SOFTWAREARG A:89binding site for residue CL A 508

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:328 -A:331

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:50 -Phe A:51
2Glu A:144 -Tyr A:145
3Ser A:261 -Pro A:262
4Asp A:316 -Pro A:317
5Trp A:403 -His A:404
6Gly A:480 -Tyr A:481

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z2H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z2H)

(-) 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:498
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeeeeeee.....ee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhhh...eeehhhhhhhhhh...eeeeee....eeeeee....eeee....hhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z2h A   2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRLA 499
                                    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       371       381       391       401       411       421       431       441       451       461       471       481       491
   Legend:   → Mismatch (orange background)
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  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 4Z2H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z2H)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)

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    Glu A:144 - Tyr A:145   [ RasMol ]  
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    Ser A:261 - Pro A:262   [ RasMol ]  
    Ser A:50 - Phe A:51   [ RasMol ]  
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  4z2h
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  CHIB_SERMA | P11797
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  3.2.1.14
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHIB_SERMA | P11797: 1e6n 1goi 1h0g 1h0i 1o6i 1ogb 1ogg 3wd0 3wd1 3wd2 3wd3 3wd4 4z2g 4z2i 4z2j 4z2k 4z2l

(-) Related Entries Specified in the PDB File

3wd0 3WD0 CONTAINS THE SAME PROTEIN.
4z2g
4z2i
4z2j
4z2k
4z2l