PDB entry 3dp8

View 3dp8 on RCSB PDB site
Description: Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (nickel butane-1,2,4-tricarboxylate form)
Class: metal transport
Keywords: Nickel, Periplasm, Nickellophore, Butane-1, 2, 4-tricarboxylate, Transport, METAL TRANSPORT
Deposited on 2008-07-07, released 2008-09-16
The last revision prior to the SCOP 1.75 freeze date was dated 2008-09-30, with a file datestamp of 2008-09-26.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.201
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nickel-binding periplasmic protein
    Species: Escherichia coli [TaxId:83333]
    Gene: nikA, b3476, JW3441
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3dp8a1
  • Chain 'B':
    Compound: Nickel-binding periplasmic protein
    Species: Escherichia coli [TaxId:83333]
    Gene: nikA, b3476, JW3441
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3dp8b1
  • Chain 'C':
    Compound: Nickel-binding periplasmic protein
    Species: Escherichia coli [TaxId:83333]
    Gene: nikA, b3476, JW3441
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d3dp8c1
  • Heterogens: NI, ACT, SO4, CL, HCT, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3dp8A (A:)
    aapdeittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedg
    ktwtftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqi
    tlksayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvr
    nenywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayht
    qlsqpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpy
    anlglkpsqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeii
    qadmrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfq
    aqqgladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpel
    gnipyapiateipfeqikpvkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dp8A (A:)
    apdeittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedgk
    twtftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqit
    lksayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvrn
    enywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayhtq
    lsqpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpya
    nlglkpsqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeiiq
    admrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfqa
    qqgladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpelg
    nipyapiateipfeqikp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3dp8B (B:)
    aapdeittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedg
    ktwtftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqi
    tlksayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvr
    nenywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayht
    qlsqpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpy
    anlglkpsqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeii
    qadmrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfq
    aqqgladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpel
    gnipyapiateipfeqikpvkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dp8B (B:)
    pdeittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedgkt
    wtftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqitl
    ksayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvrne
    nywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayhtql
    sqpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpyan
    lglkpqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeiiqad
    mrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfqaqq
    gladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpelgni
    pyapiateipfeqikpv
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3dp8C (C:)
    aapdeittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedg
    ktwtftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqi
    tlksayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvr
    nenywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayht
    qlsqpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpy
    anlglkpsqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeii
    qadmrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfq
    aqqgladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpel
    gnipyapiateipfeqikpvkp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3dp8C (C:)
    deittawpvnvgplnphlytpnqmfaqsmvyeplvkyqadgsvipwlakswthsedgktw
    tftlrddvkfsngepfdaeaaaenfravldnrqrhawlelanqivdvkalsktelqitlk
    sayypflqelalprpfrfiapsqfknhetmngikapigtgpwilqesklnqydvfvrnen
    ywgekpaikkitfnvipdpttravafetgdidllygnegllpldtfarfsqnpayhtqls
    qpietvmlalntakaptnelavrealnyavnkkslidnalygtqqvadtlfapsvpyanl
    glkpsqydpqkakallekagwtlpagkdirekngqplrielsfigtdalsksmaeiiqad
    mrqigadvsligeeessiyarqrdgrfgmifhrtwgapydphaflssmrvpshadfqaqq
    gladkplidkeigevlathdetqrqalyrdiltrlhdeavylpisyismmvvskpelgni
    pyapiateipfeqikp