PDB entry 5ypm

View 5ypm on RCSB PDB site
Description: Crystal structure of NDM-1 bound to hydrolyzed meropenem representing an EI1 complex
Class: hydrolase
Keywords: NDM-1, meropenem, EI1 complex, HYDROLASE
Deposited on 2017-11-02, released 2018-02-21
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-02-21, with a file datestamp of 2018-02-16.
Experiment type: XRAY
Resolution: 2.15 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypma_
  • Chain 'B':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmb_
  • Chain 'C':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmc_
  • Chain 'D':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmd_
  • Chain 'E':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypme_
  • Chain 'F':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmf_
  • Chain 'G':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmg_
  • Chain 'H':
    Compound: Metallo-beta-lactamase NDM-1
    Species: Escherichia coli [TaxId:562]
    Gene: blaNDM-1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d5ypmh_
  • Heterogens: ZN, 8YL, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5ypmA (A:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmA (A:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5ypmB (B:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmB (B:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5ypmC (C:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmC (C:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5ypmD (D:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmD (D:)
    gdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqi
    lnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhsl
    tfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnl
    gdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5ypmE (E:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmE (E:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >5ypmF (F:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmF (F:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >5ypmG (G:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmG (G:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >5ypmH (H:)
    geirptigqqmetgdqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlv
    vdtawtddqtaqilnwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnql
    apqegmvaaqhsltfaangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggc
    likdskakslgnlgdadtehyaasarafgaafpkasmivmshsapdsraaithtarmadk
    lr
    

    Sequence, based on observed residues (ATOM records): (download)
    >5ypmH (H:)
    dqrfgdlvfrqlapnvwqhtsyldmpgfgavasnglivrdggrvlvvdtawtddqtaqil
    nwikqeinlpvalavvthahqdkmggmdalhaagiatyanalsnqlapqegmvaaqhslt
    faangwvepatapnfgplkvfypgpghtsdnitvgidgtdiafggclikdskakslgnlg
    dadtehyaasarafgaafpkasmivmshsapdsraaithtarmadklr