PDB entry 5yol

View 5yol on RCSB PDB site
Description: Crystal structure of octameric form of Nucleoside diphosphate kinase from Acinetobacter baumannii at 2.2 A resolution
Class: transferase
Keywords: transferase
Deposited on 2017-10-29, released 2017-11-08
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-11-08, with a file datestamp of 2017-11-03.
Experiment type: XRAY
Resolution: 2.2 Å
R-factor: N/A
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yola_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yolb_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yolc_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yold_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yole_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yolf_
  • Chain 'G':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yolg_
  • Chain 'H':
    Compound: Nucleoside diphosphate kinase
    Species: ACINETOBACTER BAUMANNII [TaxId:470]
    Gene: ndk, A7A59_04275, A7M79_04705, A7M90_00500, A7N09_02655, AB895_2022, AB988_1826, AB994_3665, ABUW_3381, APD06_17770, AZE33_02560, B4R90_00300, B9X91_01430, B9X95_00285, BGC29_14850, CAS83_00635, CAS84_07305, CAT05_09960, CAT56_03875, CAT78_05970, CBE85_04645, CBI29_00577, IX87_17090, LV38_00051, NT90_02330
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5yolh_
  • Heterogens: MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolA (A:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolB (B:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolC (C:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolD (D:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolE (E:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolF (F:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolG (G:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >5yolH (H:)
maiertlsivkpdavsknhigeifarfekaglkivatkmkhlsqadaegfyaehkergff
gdlvafmtsgpvvvsvlegenavlahreilgatnpkeaapgtiradfavsidenaahgsd
svasaereiayffadneicprtr