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(-) Description

Title :  CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE SMB-1 BOUND TO HYDROLYZED DORIPENEM
 
Authors :  J. Wachino, Y. Arakawa
Date :  23 Nov 15  (Deposition) - 11 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.39
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wachino, Y. Arakawa
Crystal Structure Of Metallo-Beta-Lactamase Smb-1 Bound To Hydrolyzed Doripenem
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMB-1
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1DQM1Ligand/Ion(2~{S},3~{R},4~{S})-2-[(2~{S},3~{R})-1,3-BIS(OXIDANYL)-1-OXIDANYLIDENE-BUTAN-2-YL]-3-METHYL-4-[(3~{S},5~{S})-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL]SULFANYL-3,4-DIHYDRO-2~{H}-PYRROLE-5-CARBOXYLIC ACID
2NA7Ligand/IonSODIUM ION
3SO43Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:72 , HIS A:74 , HIS A:150 , ZN A:302 , DQM A:313 , HOH A:425binding site for residue ZN A 301
02AC2SOFTWAREASP A:76 , HIS A:77 , HIS A:215 , ZN A:301 , DQM A:313 , HOH A:425binding site for residue ZN A 302
03AC3SOFTWARESER A:82 , GLN A:85 , LYS A:86 , SER A:123 , ALA A:124 , HOH A:670binding site for residue NA A 303
04AC4SOFTWARESER A:70 , THR A:71 , ALA A:94 , GLY A:95 , GLY A:153 , ILE A:155 , HOH A:499binding site for residue NA A 304
05AC5SOFTWAREPRO A:8 , GLN A:9 , VAL A:50 , ASN A:54 , PRO A:190 , HOH A:536 , HOH A:606binding site for residue NA A 305
06AC6SOFTWAREHIS A:150 , THR A:177 , VAL A:179 , HOH A:480 , HOH A:570binding site for residue NA A 306
07AC7SOFTWAREASN A:219 , HOH A:449 , HOH A:525 , HOH A:565 , HOH A:723binding site for residue NA A 307
08AC8SOFTWAREARG A:103 , LYS A:125 , VAL A:126 , SO4 A:311 , HOH A:524binding site for residue NA A 308
09AC9SOFTWARESER A:73 , ALA A:97 , ASN A:98 , THR A:101 , PRO A:108 , HOH A:421 , HOH A:533binding site for residue NA A 309
10AD1SOFTWARELYS A:125 , ARG A:127 , THR A:177 , ARG A:252 , HOH A:407 , HOH A:429 , HOH A:447 , HOH A:458 , HOH A:476 , HOH A:520binding site for residue SO4 A 310
11AD2SOFTWAREALA A:124 , LYS A:125 , ARG A:127 , ARG A:252 , NA A:308 , HOH A:465 , HOH A:563 , HOH A:577binding site for residue SO4 A 311
12AD3SOFTWARELYS A:61 , LEU A:62 , SER A:63 , HOH A:436 , HOH A:487 , HOH A:491binding site for residue SO4 A 312
13AD4SOFTWARETRP A:5 , ASP A:76 , HIS A:77 , GLY A:89 , GLN A:113 , LYS A:125 , HIS A:150 , SER A:175 , THR A:177 , HIS A:215 , GLU A:217 , ARG A:252 , ZN A:301 , ZN A:302 , HOH A:403 , HOH A:425 , HOH A:526 , HOH A:591 , HOH A:595 , HOH A:620binding site for residue DQM A 313

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:162 -A:167
2A:208 -A:242

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B15)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B15)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B15)

(-) Exons   (0, 0)

(no "Exon" information available for 5B15)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eee........eee.....eeee.....hhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh....................eeee....eeee..eeeeeee........eeeeeeeee..eeeeeeee...........hhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b15 A   3 RDWSSPQQPFTIYGNTHYVGTGGISAVLLSSPQGHILVDGTTEKGAQVVAANIRAMGFKLSDVKYILSTHSHEDHAGGISAMQKLTGATVLAGAANVDTLRTGVSPKSDPQFGSLSNFPGSAKVRAVADGELVKLGPLAVKAHATPGHTEGGITWTWQSCEQGKCKDVVFADSLTAVSADSYRFSDHPEVVASLRGSFEAVEKLSCDIAIAAHPEVNDMWTRQQRAAKEGNSAYVDNGACRAIAAAGRKRLETRLASEK 261
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   Legend:   → Mismatch (orange background)
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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 5B15)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B15)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B15)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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UniProtKB/TrEMBL
        G5ELM3_SERMA | G5ELM3: 3vpe 3vqz 5axo 5axr 5aya 5b1u

(-) Related Entries Specified in the PDB File

5awy