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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE CARBOXYPEPTIDASE AMPC FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  Y. Kim, C. Hatzos-Skintges, M. Endres, G. Babnigg, A. Joachimiak, Midw Center For Structural Genomics (Mcsg)
Date :  01 Oct 15  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Hatzos-Skintges, M. Endres, G. Babnigg, A. Joachimiak
Crystal Structure Of D-Alanine Carboxypeptidase Ampc From Mycobacterium Smegmatis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B, C
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 27-380
    Gene: MSMEG_3978
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 34)

Asymmetric Unit (3, 34)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE27Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE9Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:185 , ARG A:243binding site for residue CL A 401
2AC2SOFTWAREGLN A:114 , PHE A:115 , HOH A:550binding site for residue CL A 402
3AC3SOFTWAREVAL B:185binding site for residue CL B 401
4AC4SOFTWAREGLN B:114 , PHE B:115 , HOH B:529binding site for residue CL B 402
5AC5SOFTWAREVAL C:185binding site for residue CL C 401
6AC6SOFTWAREGLN C:114 , PHE C:115 , HOH C:549 , HOH C:640binding site for residue CL C 402
7AC7SOFTWAREPHE C:211 , ASP C:212 , ALA C:213 , GLU C:214 , HOH C:502 , HOH C:603 , HOH C:644binding site for residue GOL C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E2H)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:270 -Pro A:271
2Tyr B:270 -Pro B:271
3Tyr C:270 -Pro C:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E2H)

(-) Exons   (0, 0)

(no "Exon" information available for 5E2H)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhh..eeeeeeee..eeeeeeee...............ee...hhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh...............hhhhhh..ee.....ee......hhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee..eee....eeee...hhhhhhhhhhhhhhhh.ee.ee........eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e2h A   0 ADPSAAVARAFAPLLDQYDVPGmAVAVTVDGRQHFYEFGVVSKQTQAPVTRDTLFEIGSVSKTFTATLAGYAATRGVLNLDDHPGRYLPALAGTPIDRAELRNLGTYTAGGLPLQFPESVTDDEQmIAYFQQFQPVTAPGKIRQYSNPSVGLLGHISARALGGQFTDLmQSQILTGLGLRRSFVDVTDEAmDFYAWGYDKKNHPVRVNPGVFDAEAYGVKSTTADmIRFIEHNIDPGALEPTLREAVKSTQVGYYKVGPmVQDLGWEQYPYPVALDQLLAGNSGEmAmSPQAATAIAPPSVGSALFNKTGSTDGFGAYAAFVPERRIGIVmLANKNFPIPARVTAAHTVLDALD 353
                                     9        19  |     29        39        49        59        69        79        89        99       109       119     | 129       139       149       159       169       179       189|      199       209       219     | 229       239       249       259       269       279     | 289       299       309       319       329|      339       349    
                                                 22-MSE                                                                                                125-MSE                                    168-MSE               190-MSE                            225-MSE                           259-MSE                   285-MSE                                      330-MSE                   
                                                                                                                                                                                                                                                                                                                         287-MSE                                                              


Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhh..eeeeeeee..eeeeeeee...............ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh...............hhhhhh..ee.....ee......hhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eee....eeee...hhhhhhhhhhhhhhhh.ee.ee........eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e2h B   0 ADPSAAVARAFAPLLDQYDVPGmAVAVTVDGRQHFYEFGVVSKQTQAPVTRDTLFEIGSVSKTFTATLAGYAATRGVLNLDDHPGRYLPALAGTPIDRAELRNLGTYTAGGLPLQFPESVTDDEQmIAYFQQFQPVTAPGKIRQYSNPSVGLLGHISARALGGQFTDLmQSQILTGLGLRRSFVDVTDEAmDFYAWGYDKKNHPVRVNPGVFDAEAYGVKSTTADmIRFIEHNIDPGALEPTLREAVKSTQVGYYKVGPmVQDLGWEQYPYPVALDQLLAGNSGEmAmSPQAATAIAPPSVGSALFNKTGSTDGFGAYAAFVPERRIGIVmLANKNFPIPARVTAAHTVLDALD 353
                                     9        19  |     29        39        49        59        69        79        89        99       109       119     | 129       139       149       159       169       179       189|      199       209       219     | 229       239       249       259       269       279     | 289       299       309       319       329|      339       349    
                                                 22-MSE                                                                                                125-MSE                                    168-MSE               190-MSE                            225-MSE                           259-MSE                   285-MSE                                      330-MSE                   
                                                                                                                                                                                                                                                                                                                         287-MSE                                                              


Chain C from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhh.hhhhhhh..eeeeeeee..eeeeeeee...............ee...hhhhhhhhhhhhhhhhh......hhhhhhhhhh.hhhhhhhhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhhh.hhhhhhhhhh...............hhhhhh..ee.....ee......hhhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eee....eeee...hhhhhhhhhhhhhhhh.ee.ee........eeeeeeee....eeeeeee....eeeeeee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5e2h C   0 ADPSAAVARAFAPLLDQYDVPGmAVAVTVDGRQHFYEFGVVSKQTQAPVTRDTLFEIGSVSKTFTATLAGYAATRGVLNLDDHPGRYLPALAGTPIDRAELRNLGTYTAGGLPLQFPESVTDDEQmIAYFQQFQPVTAPGKIRQYSNPSVGLLGHISARALGGQFTDLmQSQILTGLGLRRSFVDVTDEAmDFYAWGYDKKNHPVRVNPGVFDAEAYGVKSTTADmIRFIEHNIDPGALEPTLREAVKSTQVGYYKVGPmVQDLGWEQYPYPVALDQLLAGNSGEmAmSPQAATAIAPPSVGSALFNKTGSTDGFGAYAAFVPERRIGIVmLANKNFPIPARVTAAHTVLDALD 353
                                     9        19  |     29        39        49        59        69        79        89        99       109       119     | 129       139       149       159       169       179       189|      199       209       219     | 229       239       249       259       269       279     | 289       299       309       319       329|      339       349    
                                                 22-MSE                                                                                                125-MSE                                    168-MSE               190-MSE                            225-MSE                           259-MSE                   285-MSE                                      330-MSE                   
                                                                                                                                                                                                                                                                                                                         287-MSE
   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 5E2H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E2H)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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5e2g