PDB entry 5ypk

View 5ypk on RCSB PDB site
Description: Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI2 complex
Class: hydrolase
Keywords: NDM-1, Imipenem, EI2 complex, HYDROLASE
Deposited on 2017-11-02, released 2018-02-21
The last revision prior to the SCOPe 2.08 freeze date was dated 2018-05-16, with a file datestamp of 2018-05-11.
Experiment type: XRAY
Resolution: 2 Å
R-factor: N/A
AEROSPACI score: 0.32 (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 2.08: d5ypka_
  • 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 2.08: d5ypkb_
  • 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 2.08: d5ypkc_
  • 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 2.08: d5ypkd_
  • 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 2.08: d5ypke_
  • 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 2.08: d5ypkf_
  • 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 2.08: d5ypkg_
  • 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 2.08: d5ypkh_
  • Heterogens: HIW, ZN, SO4, NA, CL, HOH

PDB Chain Sequences:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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