PDB entry 5v6d

View 5v6d on RCSB PDB site
Description: Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate
Class: transferase
Keywords: SSGCID, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, nucleoside diphosphate kinase, TRANSFERASE
Deposited on 2017-03-16, released 2017-04-19
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-04-19, with a file datestamp of 2017-04-14.
Experiment type: XRAY
Resolution: 1.85 Å
R-factor: N/A
AEROSPACI score: 0.36 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6da_
  • Chain 'B':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6db_
  • Chain 'C':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dc_
  • Chain 'D':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dd_
  • Chain 'E':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6de_
  • Chain 'F':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6df_
  • Chain 'G':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dg_
  • Chain 'H':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dh_
  • Chain 'I':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6di_
  • Chain 'J':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dj_
  • Chain 'K':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dk_
  • Chain 'L':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dl_
  • Chain 'M':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dm_
  • Chain 'N':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dn_
  • Chain 'O':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6do_
  • Chain 'P':
    Compound: Nucleoside diphosphate kinase
    Species: Neisseria gonorrhoeae NCCP11945 [TaxId:521006]
    Gene: ndk, NGK_1320
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d5v6dp_
  • Heterogens: CIT, EDO, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >5v6dA (A:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dA (A:)
aiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfya
glvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsds
venaaleiayffsqteicpr

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >5v6dB (B:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dB (B:)
aiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfya
glvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsds
venaaleiayffsqteicpr

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >5v6dC (C:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dC (C:)
iertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfyag
lvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsdsv
enaaleiayffsqteicpr

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >5v6dD (D:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dD (D:)
aiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfya
glvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsds
venaaleiayffsqteicpr

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >5v6dE (E:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dE (E:)
iertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfyag
lvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsdsv
enaaleiayffsqteicpr

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >5v6dF (F:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dF (F:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >5v6dG (G:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dG (G:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >5v6dH (H:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dH (H:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >5v6dI (I:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dI (I:)
aiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfya
glvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsds
venaaleiayffsqteicpr

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >5v6dJ (J:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dJ (J:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >5v6dK (K:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dK (K:)
aiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfya
glvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsds
venaaleiayffsqteicpr

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >5v6dL (L:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dL (L:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >5v6dM (M:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dM (M:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >5v6dN (N:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dN (N:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr

  • Chain 'O':
    Sequence, based on SEQRES records: (download) 
    >5v6dO (O:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dO (O:)
iertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfyag
lvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsdsv
enaaleiayffsqteicpr

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >5v6dP (P:)
mahhhhhhmaiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefya
vhkdrpfyaglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvs
inavhgsdsvenaaleiayffsqteicpr

    Sequence, based on observed residues (ATOM records): (download) 
    >5v6dP (P:)
maiertisiikpdavgknvigkiysrfeenglkivaakmkqltlkeaqefyavhkdrpfy
aglvefmtggpvmiqvlegenavlknrelmgatnpteaaegtiradfatsvsinavhgsd
svenaaleiayffsqteicpr