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(-) Description

Title :  SERRATIA MARCESCENS CHITINASE B COMPLEXED WITH AZIDE INHIBITOR
 
Authors :  T. Hirose, N. Maita, H. Gouda, J. Koseki, T. Yamamoto, A. Sugawara, H. Na S. Hirono, K. Shiomi, T. Watanabe, H. Taniguchi, K. B. Sharpless, S. Om T. Sunazuka
Date :  06 Jun 13  (Deposition) - 18 Sep 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Tim Barrel, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hirose, N. Maita, H. Gouda, J. Koseki, T. Yamamoto, A. Sugawara, H. Nakano, S. Hirono, K. Shiomi, T. Watanabe, H. Taniguchi, K. B. Sharpless, S. Omura, T. Sunazuka
Observation Of The Controlled Assembly Of Preclick Components In The In Situ Click Chemistry Generation Of A Chitinase Inhibitor
Proc. Natl. Acad. Sci. Usa V. 110 15892 2013
PubMed-ID: 24043811  |  Reference-DOI: 10.1073/PNAS.1315049110

(-) Compounds

Molecule 1 - CHITINASE B
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHIS B
    Expression System Strain: DH5A
    Expression System Taxid: 562
    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, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1A1L1Ligand/Ion[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE
2GOL9Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1A1L1Ligand/Ion[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE
2GOL9Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 22)
No.NameCountTypeFull Name
1A1L2Ligand/Ion[2-[[(2S)-1-[BIS(PHENYLMETHYL)AMINO]-5-[[N-(METHYLCARBAMOYL)CARBAMIMIDOYL]AMINO]-1-OXIDANYLIDENE-PENTAN-2-YL]AMINO]-2-OXIDANYLIDENE-ETHYL]-DIAZONIO-AZANIDE
2GOL18Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:10 , TRP A:97 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , PRO A:219 , TRP A:220 , TYR A:292 , ARG A:294 , ASP A:316 , ARG A:338 , ILE A:339 , TRP A:403 , GLN A:407 , HOH A:881BINDING SITE FOR RESIDUE A1L A 501
02AC2SOFTWAREARG A:4 , HIS A:46 , ARG A:89 , HOH A:675 , HOH A:932BINDING SITE FOR RESIDUE GOL A 502
03AC3SOFTWAREPRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:648 , HOH A:748BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWAREARG A:244 , TRP A:252 , PHE A:259 , PRO A:260 , SER A:261 , HOH A:784 , HOH A:849BINDING SITE FOR RESIDUE GOL A 504
05AC5SOFTWARETYR A:323 , LEU A:325 , VAL A:326 , GLY A:327 , CYS A:328 , ASP A:329 , VAL A:332 , HOH A:678BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREARG A:162 , ALA A:204 , PRO A:205 , ASP A:207 , LYS A:284BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWARELYS A:393 , TYR A:421 , TYR A:427 , ASP A:428 , ASP A:429 , SER A:430 , HOH A:761BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWARETRP A:359 , ASN A:360 , ASP A:361 , HOH A:654 , HOH A:869BINDING SITE FOR RESIDUE GOL A 508
09AC9SOFTWAREALA A:463 , GLN A:464 , GLY A:480 , TYR A:481BINDING SITE FOR RESIDUE GOL A 509
10BC1SOFTWARETYR A:391 , GLN A:394 , GLN A:395 , ARG A:439 , HOH A:829 , HOH A:847BINDING SITE FOR RESIDUE GOL A 510
11BC2SOFTWARELYS A:386 , ARG A:420 , HOH A:896BINDING SITE FOR RESIDUE SO4 A 511

(-) 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 3WD3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIB_SERMA136-144  1A:136-144
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIB_SERMA136-144  1A:136-144
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIB_SERMA136-144  2A:136-144

(-) Exons   (0, 0)

(no "Exon" information available for 3WD3)

(-) 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:497
 aligned with CHIB_SERMA | P11797 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:497
                                    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       
           CHIB_SERMA     2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRL 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.eeeee...............................hhhhhhh....eeehhhhhhhhhh...eeeeee....eeeeee....eeee....hhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wd3 A   2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRL 498
                                    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)
  - → 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 3WD3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WD3)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHIB_SERMA | P11797)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3wd3
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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 3wd4 4z2g 4z2h 4z2i 4z2j 4z2k 4z2l

(-) Related Entries Specified in the PDB File

3wd0 3wd1 3wd2 3wd4