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(-) Description

Title :  CRYSTAL STRUCTURE OF AMPC BETA-LACTAMASE IN COMPLEX WITH FRAGMENT 50 (N-(METHYLSULFONYL)-N-PHENYL-ALANINE)
 
Authors :  O. Eidam, S. Barelier, I. Fish, B. K. Shoichet
Date :  29 May 13  (Deposition) - 21 May 14  (Release) - 30 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ampc Beta-Lactamase, Class C, Hydrolase, Cephalosporinase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Barelier, O. Eidam, I. Fish, J. Hollander, F. Figaroa, R. Nachane, J. J. Irwin, B. K. Shoichet, G. Siegal
Increasing Chemical Space Coverage By Combining Empirical And Computational Fragment Screens.
Acs Chem. Biol. V. 9 1528 2014
PubMed-ID: 24807704  |  Reference-DOI: 10.1021/CB5001636

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POGO295
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 20-377
    Gene: AMPA, AMPC, B4150, JW4111
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: AMPC BETA-LACTAMASE, CEPHALOSPORINASE

 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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1NZ25Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-L-ALANINE
2NZ32Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-D-ALANINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1NZ23Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-L-ALANINE
2NZ31Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-D-ALANINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NZ22Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-L-ALANINE
2NZ31Ligand/IonN-(METHYLSULFONYL)-N-PHENYL-D-ALANINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:64 , GLN A:120 , ASN A:152 , TYR A:221 , GLY A:317 , ALA A:318 , THR A:319 , ASN A:343 , NZ2 A:404 , HOH A:519 , HOH A:904BINDING SITE FOR RESIDUE NZ2 A 401
2AC2SOFTWAREASN A:237 , LEU A:238 , LYS A:239 , PRO A:240 , LEU A:241 , GLN A:256 , ALA A:307 , PRO A:330 , HOH A:579 , HOH A:586 , HOH A:777 , HOH A:913 , HOH B:805BINDING SITE FOR RESIDUE NZ2 A 402
3AC3SOFTWARELEU A:238 , LYS A:239 , PRO A:240 , LEU A:241 , GLN A:256 , ALA A:307 , ARG A:309 , PRO A:330 , GLU A:331 , HOH A:586 , HOH A:594 , HOH A:913BINDING SITE FOR RESIDUE NZ3 A 403
4AC4SOFTWAREGLN A:120 , VAL A:211 , SER A:212 , TYR A:221 , THR A:319 , GLY A:320 , NZ2 A:401 , HOH A:570 , HOH A:593 , HOH A:806BINDING SITE FOR RESIDUE NZ2 A 404
5AC5SOFTWARESER B:64 , GLN B:120 , ASN B:152 , TYR B:221 , GLY B:317 , ALA B:318 , THR B:319 , ASN B:343 , NZ2 B:403 , HOH B:569 , HOH B:766BINDING SITE FOR RESIDUE NZ2 B 401
6AC6SOFTWARELYS A:246 , ASN B:237 , LEU B:238 , LYS B:239 , PRO B:240 , LEU B:241 , GLN B:256 , ALA B:307 , ARG B:309 , PRO B:330 , HOH B:537 , HOH B:555 , HOH B:745 , HOH B:815BINDING SITE FOR RESIDUE NZ3 B 402
7AC7SOFTWAREGLN B:120 , VAL B:211 , SER B:212 , TYR B:221 , THR B:319 , GLY B:320 , NZ2 B:401 , HOH B:578 , HOH B:698BINDING SITE FOR RESIDUE NZ2 B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:276 -Pro A:277
2Thr A:302 -Pro A:303
3Trp B:276 -Pro B:277
4Thr B:302 -Pro B:303

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KZB)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhh.............hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeeee..eeeeeeeehhh.eeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kzb A   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353        


Chain B from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhh....hhhhh..hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhh.....hhhhhhhhhh.............hhhhhhhh..eee..eee......hhhhhhh.eehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.eeeee..eee....eeee...hhhhhhhhhhhhhhh..ee.eeeeeee.....eeeeeeeee..eeeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kzb B   4 APQQINDIVHRTITPLIEQQKIPGMAVAVIYQGKPYYFTWGYADIAKKQPVTQQTLFELGSVSKTFTGVLGGDAIARGEIKLSDPTTKYWPELTAKQWNGITLLHLATYTAGGLPLQVPDEVKSSSDLLRFYQNWQPAWAPGTQRLYANSSIGLFGALAVKPSGLSFEQAMQTRVFQPLKLNHTWINVPPAEEKNYAWGYREGKAVHVSPGALDAEAYGVKSTIEDMARWVQSNLKPLDINEKTLQQGIQLAQSRYWQTGDMYQGLGWEMLDWPVNPDSIINGSDNKIALAARPVKAITPPTPAVRASWVHKTGATGGFGSYVAFIPEKELGIVMLANKNYPNPARVDAAWQILNALQ 361
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   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 4KZB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
        AMPC_ECOLI | P00811: 1c3b 1fcm 1fcn 1fco 1fsw 1fsy 1ga9 1i5q 1iel 1iem 1kds 1kdw 1ke0 1ke3 1ke4 1kvl 1kvm 1l0d 1l0e 1l0f 1l0g 1l2s 1ll5 1ll9 1llb 1mxo 1my8 1o07 1pi4 1pi5 1xgi 1xgj 2bls 2ffy 2hdq 2hdr 2hds 2hdu 2i72 2p9v 2pu2 2pu4 2r9w 2r9x 2rcx 3bls 3bm6 3fkv 3fkw 3gqz 3gr2 3grj 3gsg 3gtc 3gv9 3gvb 3iwi 3iwo 3iwq 3ixb 3ixd 3ixg 3ixh 3o86 3o87 3o88 4e3i 4e3j 4e3k 4e3l 4e3m 4e3n 4e3o 4jxg 4jxs 4jxv 4jxw 4ken 4kg2 4kg5 4kg6 4kz3 4kz4 4kz5 4kz6 4kz7 4kz8 4kz9 4kza 4lv0 4lv1 4lv2 4lv3 4okp 4old 4olg

(-) Related Entries Specified in the PDB File

4kz3 4kz4 4kz5 4kz6 4kz7 4kz8 4kz9 4kza