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(-) Description

Title :  AMCASE IN COMPLEX WITH COMPOUND 1
 
Authors :  A. Olland
Date :  20 Apr 11  (Deposition) - 24 Aug 11  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. C. Cole, A. M. Olland, J. Jacob, J. Brooks, M. G. Bursavich, R. Czerwinski, C. Declercq, M. Johnson, D. Joseph-Mccarthy, J. W. Ellingboe, L. Lin, P. Nowak, E. Presman, J. Strand, A. Tam, C. M. M. Williams, S. Yao, D. H. H. Tsao, L. J. Fitz
Identification And Characterization Of Acidic Mammalian Chitinase Inhibitors
J. Med. Chem. V. 53 6122 2010
PubMed-ID: 20666458

(-) Compounds

Molecule 1 - ACIDIC MAMMALIAN CHITINASE
    ChainsA, B
    EC Number3.2.1.14
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineOVARY
    Expression System CommonCHINESE HAMSTER
    Expression System Taxid10029
    FragmentCATALYTIC DOMAIN RESIDUES 22-408
    GeneCHIA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAMCASE, LUNG-SPECIFIC PROTEIN TSA1902

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13RM2Ligand/Ion5-{4-[2-(4-BROMOPHENOXY)ETHYL]PIPERAZIN-1-YL}-4H-1,2,4-TRIAZOL-3-AMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13RM1Ligand/Ion5-{4-[2-(4-BROMOPHENOXY)ETHYL]PIPERAZIN-1-YL}-4H-1,2,4-TRIAZOL-3-AMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13RM1Ligand/Ion5-{4-[2-(4-BROMOPHENOXY)ETHYL]PIPERAZIN-1-YL}-4H-1,2,4-TRIAZOL-3-AMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:27 , ASP A:138 , GLU A:140 , ALA A:183 , MET A:210 , TYR A:212 , ASP A:213 , TYR A:267 , ALA A:295 , GLU A:297 , ILE A:300 , TRP A:360 , LEU A:364 , HOH A:635BINDING SITE FOR RESIDUE 3RM A 1
2AC2SOFTWARETYR B:27 , ASP B:138 , GLU B:140 , ALA B:183 , MET B:210 , TYR B:212 , ASP B:213 , TYR B:267 , ALA B:295 , GLU B:297 , ILE B:300 , TRP B:360 , HOH B:635BINDING SITE FOR RESIDUE 3RM B 1

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:26 -A:51
2A:49 -A:394
3A:307 -A:372
4B:26 -B:51
5B:49 -B:394
6B:307 -B:372

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ala A:57 -Phe A:58
2Glu A:140 -Tyr A:141
3Trp A:360 -Ala A:361
4Ala B:57 -Phe B:58
5Glu B:140 -Tyr B:141
6Trp B:360 -Ala B:361

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 18)

Asymmetric Unit (9, 18)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063030N45DCHIA_HUMANPolymorphism41282492A/BD45D
2UniProtVAR_063031D47NCHIA_HUMANPolymorphism41282494A/BN47N
3UniProtVAR_063032R61MCHIA_HUMANPolymorphism41282496A/BM61M
4UniProtVAR_049192G102RCHIA_HUMANPolymorphism3818822A/BG102R
5UniProtVAR_063033K125RCHIA_HUMANPolymorphism61756687A/BK125R
6UniProtVAR_033730V324GCHIA_HUMANPolymorphism2256721A/BV324G
7UniProtVAR_049193I339VCHIA_HUMANPolymorphism2275253A/BV339V
8UniProtVAR_049194F354SCHIA_HUMANPolymorphism2275254A/BF354S
9UniProtVAR_049195F377LCHIA_HUMANPolymorphism36011905A/BF377L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063030N45DCHIA_HUMANPolymorphism41282492AD45D
2UniProtVAR_063031D47NCHIA_HUMANPolymorphism41282494AN47N
3UniProtVAR_063032R61MCHIA_HUMANPolymorphism41282496AM61M
4UniProtVAR_049192G102RCHIA_HUMANPolymorphism3818822AG102R
5UniProtVAR_063033K125RCHIA_HUMANPolymorphism61756687AK125R
6UniProtVAR_033730V324GCHIA_HUMANPolymorphism2256721AV324G
7UniProtVAR_049193I339VCHIA_HUMANPolymorphism2275253AV339V
8UniProtVAR_049194F354SCHIA_HUMANPolymorphism2275254AF354S
9UniProtVAR_049195F377LCHIA_HUMANPolymorphism36011905AF377L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063030N45DCHIA_HUMANPolymorphism41282492BD45D
2UniProtVAR_063031D47NCHIA_HUMANPolymorphism41282494BN47N
3UniProtVAR_063032R61MCHIA_HUMANPolymorphism41282496BM61M
4UniProtVAR_049192G102RCHIA_HUMANPolymorphism3818822BG102R
5UniProtVAR_063033K125RCHIA_HUMANPolymorphism61756687BK125R
6UniProtVAR_033730V324GCHIA_HUMANPolymorphism2256721BV324G
7UniProtVAR_049193I339VCHIA_HUMANPolymorphism2275253BV339V
8UniProtVAR_049194F354SCHIA_HUMANPolymorphism2275254BF354S
9UniProtVAR_049195F377LCHIA_HUMANPolymorphism36011905BF377L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA_HUMAN132-140
 
  2A:132-140
B:132-140
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA_HUMAN132-140
 
  1A:132-140
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA_HUMAN132-140
 
  1-
B:132-140

(-) Exons   (0, 0)

(no "Exon" information available for 3RM4)

(-) 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:373
 aligned with CHIA_HUMAN | Q9BZP6 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:373
                                    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   
           CHIA_HUMAN    22 YQLTCYFTNWAQYRPGLGRFMPDNIDPCLCTHLIYAFAGRQNNEITTIEWNDVTLYQAFNGLKNKNSQLKTLLAIGGWNFGTAPFTAMVSTPENRQTFITSVIKFLRQYEFDGLDFDWEYPGSRGSPPQDKHLFTVLVQEMREAFEQEAKQINKPRLMVTAAVAAGISNIQSGYEIPQLSQYLDYIHVMTYDLHGSWEGYTGENSPLYKYPTDTGSNAYLNVDYVMNYWKDNGAPAEKLIVGFPTYGHNFILSNPSNTGIGAPTSGAGPAGPYAKESGIWAYYEICTFLKNGATQGWDAPQEVPYAYQGNVWVGYDNIKSFDIKAQWLKHNKFGGAMVWAIDLDDFTGTFCNQGKFPLISTLKKALGLQSASC 394
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeeee..eee....hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeee......hhhhh..............hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.eeeeeee...........eeee...........eeehhhhhhhhhh..eeeee....eeeeee..eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh...........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------D-N-------------M----------------------------------------R----------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------V--------------S----------------------L----------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------CHITINASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rm4 A  22 YQLTCYFTNWAQYRPGLGRFMPDDINPCLCTHLIYAFAGMQNNEITTIEWNDVTLYQAFNGLKNKNSQLKTLLAIGGWNFGTAPFTAMVSTPENRQTFITSVIKFLRQYEFDGLDFDWEYPGSRGSPPQDKHLFTVLVQEMREAFEQEAKQINKPRLMVTAAVAAGISNIQSGYEIPQLSQYLDYIHVMTYDLHGSWEGYTGENSPLYKYPTDTGSNAYLNVDYVMNYWKDNGAPAEKLIVGFPTYGHNFILSNPSNTGIGAPTSGAGPAGPYAKESGIWAYYEICTFLKNGATQGWDAPQEVPYAYQGNVWVGYDNVKSFDIKAQWLKHNKFGGAMVWAIDLDDFTGTFCNQGKFPLISTLKKALGLQSASC 394
                                    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   

Chain B from PDB  Type:PROTEIN  Length:377
 aligned with CHIA_HUMAN | Q9BZP6 from UniProtKB/Swiss-Prot  Length:476

    Alignment length:377
                                    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       
           CHIA_HUMAN    22 YQLTCYFTNWAQYRPGLGRFMPDNIDPCLCTHLIYAFAGRQNNEITTIEWNDVTLYQAFNGLKNKNSQLKTLLAIGGWNFGTAPFTAMVSTPENRQTFITSVIKFLRQYEFDGLDFDWEYPGSRGSPPQDKHLFTVLVQEMREAFEQEAKQINKPRLMVTAAVAAGISNIQSGYEIPQLSQYLDYIHVMTYDLHGSWEGYTGENSPLYKYPTDTGSNAYLNVDYVMNYWKDNGAPAEKLIVGFPTYGHNFILSNPSNTGIGAPTSGAGPAGPYAKESGIWAYYEICTFLKNGATQGWDAPQEVPYAYQGNVWVGYDNIKSFDIKAQWLKHNKFGGAMVWAIDLDDFTGTFCNQGKFPLISTLKKALGLQSASCTAPA 398
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeeee..eee....hhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeee......hhhhh..............hhhhhhhhhhhhhhhhhhh..hhh.eeeeee.eeeeeee...........eeee...........eeehhhhhhhhhh..eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeee.hhhh...........hhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -----------------------D-N-------------M----------------------------------------R----------------------R------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G--------------V--------------S----------------------L--------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rm4 B  22 YQLTCYFTNWAQYRPGLGRFMPDDINPCLCTHLIYAFAGMQNNEITTIEWNDVTLYQAFNGLKNKNSQLKTLLAIGGWNFGTAPFTAMVSTPENRQTFITSVIKFLRQYEFDGLDFDWEYPGSRGSPPQDKHLFTVLVQEMREAFEQEAKQINKPRLMVTAAVAAGISNIQSGYEIPQLSQYLDYIHVMTYDLHGSWEGYTGENSPLYKYPTDTGSNAYLNVDYVMNYWKDNGAPAEKLIVGFPTYGHNFILSNPSNTGIGAPTSGAGPAGPYAKESGIWAYYEICTFLKNGATQGWDAPQEVPYAYQGNVWVGYDNVKSFDIKAQWLKHNKFGGAMVWAIDLDDFTGTFCNQGKFPLISTLKKALGLQSASCTAPA 398
                                    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       

   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 3RM4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RM4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RM4)

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (CHIA_HUMAN | Q9BZP6)
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:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    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.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0003796    lysozyme activity    Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0006037    cell wall chitin metabolic process    The chemical reactions and pathways involving cell wall chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues, found in the walls of cells.
    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:0006030    chitin metabolic process    The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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.
    GO:0090197    positive regulation of chemokine secretion    Any process that increases the rate, frequency or extent of chemokine secretion, the regulated release of chemokines from a cell.
    GO:0002532    production of molecular mediator involved in inflammatory response    The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0009620    response to fungus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHIA_HUMAN | Q9BZP62ybt 2ybu 3fxy 3fy1 3rm8 3rm9 3rme

(-) Related Entries Specified in the PDB File

3rm8 3rm9 3rme