PDB entry 6ay1

View 6ay1 on RCSB PDB site
Description: Crystal structure of a nucleoside diphosphate kinase NDK from Helicobacter pylori
Class: transferase
Keywords: NIAID, structural genomics, NDK, NDPK, kinase, ATP-dependent, Seattle Structural Genomics Center for Infectious Disease, SSGCID, TRANSFERASE
Deposited on 2017-09-07, released 2017-09-20
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-09-20, with a file datestamp of 2017-09-15.
Experiment type: XRAY
Resolution: 2.05 Å
R-factor: N/A
AEROSPACI score: 0.31 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed):
    • Uniprot B5Z9W9 (8-144)
      • expression tag (7)
    Domains in SCOPe 2.08: d6ay1a1, d6ay1a2
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1b_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1c_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1d_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1e_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1g_
  • Chain 'H':
    Compound: Nucleoside diphosphate kinase
    Species: Helicobacter pylori [TaxId:210]
    Gene: ndk, HPG27_182
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6ay1h_
  • Heterogens: IPA, MPD, HEZ, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6ay1A (A:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1A (A:)
hmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpff
kdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesidanavhgsd
slenahneiafffaardl

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6ay1B (B:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1B (B:)
mkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffk
dliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesidanavhgsds
lenahneiafffaardl

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6ay1C (C:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1C (C:)
mkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffk
dliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesidanavhgsds
lenahneiafffaardl

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6ay1D (D:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1D (D:)
mkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffk
dliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesidanavhgsds
lenahneiafffaardl

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6ay1E (E:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1E (E:)
kqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffkd
liefmvsgpvvvmvlegkdavaknrdlmgatdpklagtiradfaesidanavhgsdslen
ahneiafffaardl

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6ay1G (G:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1G (G:)
kqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffkd
liefmvsgpvvvmvlegkdavaknrdlmtdpgtiradfaesidanavhgsdslenahnei
afffaardl

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6ay1H (H:)
mahhhhhhmkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyai
hrerpffkdliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesida
navhgsdslenahneiafffaardl

    Sequence, based on observed residues (ATOM records): (download) 
    >6ay1H (H:)
mkqrtlsiikpdalkkkvvgkiidrfesngleviamkrlhlsvkdaenfyaihrerpffk
dliefmvsgpvvvmvlegkdavaknrdlmgatdpklaqkgtiradfaesidanavhgsds
lenahneiafffaardl