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(-) Description

Title :  CRYSTAL STRUCTURE OF BETA-LACTAMASE PENP MUTANT-E166H IN COMPLEX WITH CEPHALORIDINE AS "PRE-DEACYLATION" INTERMEDIATE
 
Authors :  X. Pan, Y. Zhao
Date :  21 Jun 16  (Deposition) - 25 Jan 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Pan, Y. He, J. Lei, X. Huang, Y. Zhao
Crystallographic Snapshots Of Class A Beta-Lactamase Catalysis Reveal Structural Changes That Facilitate Beta-Lactam Hydrolysis
J. Biol. Chem. V. 292 4022 2017
PubMed-ID: 28100776  |  Reference-DOI: 10.1074/JBC.M116.764340

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: B, A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-307
    Gene: PENP, BLAP
    Mutation: YES
    Organism Scientific: BACILLUS LICHENIFORMIS
    Organism Taxid: 1402
    Synonym: PENICILLINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CED2Ligand/Ion5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CED1Ligand/Ion5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CED1Ligand/Ion5-METHYL-2-[2-OXO-1-(2-THIOPHEN-2-YL-ACETYLAMINO)-ETHYL]-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:69 , SER B:70 , SER B:130 , ASN B:132 , ASN B:170 , LYS B:234 , THR B:235 , GLY B:236 , ALA B:237 , ARG B:244 , HOH B:412 , HOH B:413 , HOH B:442binding site for residue CED B 301
2AC2SOFTWAREALA A:69 , SER A:70 , SER A:130 , ASN A:132 , ASN A:170 , LYS A:234 , THR A:235 , GLY A:236 , ALA A:237 , ARG A:244 , HOH A:406 , HOH A:446 , HOH A:484 , ASP B:114binding site for residue CED A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His B:166 -Pro B:167
2His A:166 -Pro A:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GHZ)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeeeeee.....eeee.....ee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ghz A  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFHPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254                                     


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..eeeeeeee.....eeee....eee...hhhhhhhhhhhhhh.hhhhh.ee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee......eeeeeeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ghz B  31 DDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFHPELNEVNPGETQDTSTARALVTSLRAFALEDKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALN 291
                                    40        50      ||61        71        81 ||     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    || 244       255       265       275       285      
                                                     57|                      83|                                                                                                                                                     238|         252|                                     
                                                      59                       86                                                                                                                                                      240          254
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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 5GHZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAC_BACLI | P00808: 1i2s 1i2w 1mbl 1w7f 2blm 2wk0 2y91 3b3x 3ly3 3ly4 3m2j 3m2k 3sh7 3sh8 3sh9 3soi 4blm 4m3k 4n1h 4n92 4n9k 4n9l 5ghx 5ghy

(-) Related Entries Specified in the PDB File

5ghx 5ghy