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(-) Description

Title :  THE CRYSTAL STRUCTURE OF AN AMIDOHYDROLASE 2 FROM PLANCTOMYCES LIMNOPHILUS DSM 3776
 
Authors :  Y. Fan, K. Tan, R. Wu, J. Bearden, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  30 Nov 12  (Deposition) - 06 Feb 13  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fan, K. Tan, R. Wu, J. Bearden, A. Joachimiak
The Crystal Structure Of An Amidohydrolase 2 From Planctomyces Limnophilus Dsm 3776
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMIDOHYDROLASE 2
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PLANCTOMYCES LIMNOPHILUS, PLIM_2160
    Organism Scientific: PLANCTOMYCES LIMNOPHILUS
    Organism Taxid: 521674
    Strain: DSM 3776

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 34)

Asymmetric/Biological Unit (4, 34)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL10Ligand/IonGLYCEROL
3MSE19Mod. Amino AcidSELENOMETHIONINE
4ZN3Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:25 , HIS A:27 , ASP A:374 , HOH A:696 , HOH A:697BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREASP A:165 , PHE A:169 , HIS A:170 , SER A:216 , PRO A:218 , ARG A:279BINDING SITE FOR RESIDUE GOL A 502
03AC3SOFTWARETYR A:44 , HIS A:45 , TYR A:46 , TRP A:344 , HOH A:697BINDING SITE FOR RESIDUE GOL A 503
04AC4SOFTWARELYS A:89BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREASP A:104 , ARG B:404 , TRP B:406 , ARG B:410BINDING SITE FOR RESIDUE ACT A 505
06AC6SOFTWAREHIS B:25 , HIS B:27 , ASP B:374 , HOH B:660 , HOH B:662BINDING SITE FOR RESIDUE ZN B 501
07AC7SOFTWAREASP B:165 , PHE B:169 , HIS B:170 , SER B:216 , ARG B:279BINDING SITE FOR RESIDUE GOL B 502
08AC8SOFTWARELYS B:313 , PRO B:335 , HOH B:674BINDING SITE FOR RESIDUE GOL B 503
09AC9SOFTWARELEU B:167 , VAL B:168 , PHE B:169 , HIS B:170 , LEU B:171 , GLN B:172 , SER B:249 , LEU B:252 , SER B:253 , HOH B:686BINDING SITE FOR RESIDUE GOL B 504
10BC1SOFTWAREALA B:80 , HIS B:81 , ARG C:365 , ASN C:366 , GLN C:417BINDING SITE FOR RESIDUE GOL B 505
11BC2SOFTWAREHIS C:25 , HIS C:27 , ASP C:374 , HOH C:736BINDING SITE FOR RESIDUE ZN C 501
12BC3SOFTWAREASP A:147 , PRO A:149 , LYS A:182 , SER C:123BINDING SITE FOR RESIDUE GOL C 502
13BC4SOFTWAREASP C:17 , GLU C:18 , ARG C:97 , GLN C:136BINDING SITE FOR RESIDUE GOL C 503
14BC5SOFTWARETYR C:44 , HIS C:45 , TYR C:46 , TRP C:344 , ASP C:374BINDING SITE FOR RESIDUE GOL C 504
15BC6SOFTWAREARG A:365 , ASN A:366 , GLN A:417 , ALA C:80 , HIS C:81 , HOH C:676BINDING SITE FOR RESIDUE GOL C 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I6V)

(-) Exons   (0, 0)

(no "Exon" information available for 4I6V)

(-) 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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eee.............hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhh.eeeee................ee.eeehhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..eeeee......................hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6v A   6 SSPIDQLCAQLDEIVLIDPHSHINPHAAASKNLGDILGYHYFTELAHSAGmPREVIEAPGITAKEKVGRIVEGLAHLDNTIQVKWLIELCERFFGFQDDRLTPDNWEALYDHSEKLmSAPDWEQTVLQKSQLEAVFLTNDFDDPLTGFDTKKYIPCLRTDDLVFHLQKPEVRQRLAKATGFDCATPAKLIHAIGQLFTHFVSHGAKACAISLPPDFEPTPVSHVDAEGPLRAAYAGHVLTTEQSQILSRFVFWTIAEFCSEHHLPFDLmIGVNRRVYESGVYQGQDLFDQRVSLYQYRRLFNAFPRVKFPISVLAHASNmELVSYAWIFPNVIANGHWWYSNIPAFIEPDCRSRLEAIPRNKNIGYYSDmYKLEFGWPKFQmYRRVLAKVLFEDFVVGRHWSEERAVELGRQILRGNVETIFSGA 430
                                    15        25        35        45        55|       65        75        85        95       105       115      |125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385 |     395       405       415       425     
                                                                             56-MSE                                                           122-MSE                                                                                                                                                 274-MSE                                            325-MSE                                           375-MSE     387-MSE                                       


Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh..eee.............hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhh.eeeee................ee.eeehhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..eeeee.ee.............ee....hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhh.ee.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6v B   1 mIATKSSPIDQLCAQLDEIVLIDPHSHINPHAAASKNLGDILGYHYFTELAHSAGmPREVIEAPGITAKEKVGRIVEGLAHLDNTIQVKWLIELCERFFGFQDDRLTPDNWEALYDHSEKLmSAPDWEQTVLQKSQLEAVFLTNDFDDPLTGFDTKKYIPCLRTDDLVFHLQKPEVRQRLAKATGFDCATPAKLIHAIGQLFTHFVSHGAKACAISLPPDFEPTPVSHVDAEGPLRAAYAGHVLTTEQSQILSRFVFWTIAEFCSEHHLPFDLmIGVNRRVYESGVYQGQDLFDQRVSLYQYRRLFNAFPRVKFPISVLAHASNmELVSYAWIFPNVIANGHWWYSNIPAFIEPDCRSRLEAIPRNKNIGYYSDmYKLEFGWPKFQmYRRVLAKVLFEDFVVGRHWSEERAVELGRQILRGNVETIFSGA 430
                            |       10        20        30        40        50     |  60        70        80        90       100       110       120 |     130       140       150       160       170       180       190       200       210       220       230       240       250       260       270   |   280       290       300       310       320    |  330       340       350       360       370    |  380      |390       400       410       420       430
                            1-MSE                                                 56-MSE                                                           122-MSE                                                                                                                                                 274-MSE                                            325-MSE                                           375-MSE     387-MSE                                       


Chain C from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eee.............hhhhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh..hhhhhhhhhh.eeeee................ee.eeehhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeee......................hhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhh....ee.......hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i6v C   6 SSPIDQLCAQLDEIVLIDPHSHINPHAAASKNLGDILGYHYFTELAHSAGmPREVIEAPGITAKEKVGRIVEGLAHLDNTIQVKWLIELCERFFGFQDDRLTPDNWEALYDHSEKLmSAPDWEQTVLQKSQLEAVFLTNDFDDPLTGFDTKKYIPCLRTDDLVFHLQKPEVRQRLAKATGFDCATPAKLIHAIGQLFTHFVSHGAKACAISLPPDFEPTPVSHVDAEGPLRAAYAGHVLTTEQSQILSRFVFWTIAEFCSEHHLPFDLmIGVNRRVYESGVYQGQDLFDQRVSLYQYRRLFNAFPRVKFPISVLAHASNmELVSYAWIFPNVIANGHWWYSNIPAFIEPDCRSRLEAIPRNKNIGYYSDmYKLEFGWPKFQmYRRVLAKVLFEDFVVGRHWSEERAVELGRQILRGNVETIFSGA 430
                                    15        25        35        45        55|       65        75        85        95       105       115      |125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385 |     395       405       415       425     
                                                                             56-MSE                                                           122-MSE                                                                                                                                                 274-MSE                                            325-MSE                                           375-MSE     387-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4I6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I6V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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