PDB entry 3q8y

View 3q8y on RCSB PDB site
Description: Crystal structure of Staphylococcus aureus nucleoside diphosphate kinase complexed with ADP and Vanadate
Class: transferase
Keywords: Ferridoxin fold, alpha-beta protein family, Nucleoside diphosphate kinases (NDKs), gamma phosphate, nucleoside triphosphates, nucleoside diphosphate, Nucleotide binding, Magnesium, Metal binding, Phosphorylation, TRANSFERASE
Deposited on 2011-01-07, released 2011-07-27
The last revision prior to the SCOPe 2.03 freeze date was dated 2011-07-27, with a file datestamp of 2011-07-22.
Experiment type: XRAY
Resolution: 2.7 Å
R-factor: 0.252
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8ya_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yb_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yc_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yd_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8ye_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yf_
  • Chain 'G':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yg_
  • Chain 'H':
    Compound: Nucleoside diphosphate kinase
    Species: Staphylococcus aureus subsp. aureus [TaxId:46170]
    Gene: ndk, SACOL1509
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d3q8yh_
  • Heterogens: ADP, VO4, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3q8yA (A:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yA (A:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3q8yB (B:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yB (B:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3q8yC (C:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yC (C:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3q8yD (D:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yD (D:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3q8yE (E:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yE (E:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3q8yF (F:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yF (F:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3q8yG (G:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yG (G:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3q8yH (H:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlyelehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3q8yH (H:)
    mertflmikpdavqrnligevisrierkglklvggklmqvpmelaethygehqgkpfynd
    lisfitsapvfamvvegedavnvsrhiigstnpseaspgsirgdlgltvgrniihgsdsl
    esaereinlwfneneitsyasprdawlye