PDB entry 6ykb

View 6ykb on RCSB PDB site
Description: [Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution
Class: oxidoreductase
Keywords: [Fe]-hydrogenase; FeGP cofactor; guanylylpyridinol; conformational changes; GMP, OXIDOREDUCTASE
Deposited on 2020-04-06, released 2021-02-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-17, with a file datestamp of 2021-02-12.
Experiment type: XRAY
Resolution: 1.55 Å
R-factor: N/A
AEROSPACI score: 0.54 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: 5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase
    Species: Methanolacinia paynteri G-2000 [TaxId:694436]
    Gene: hmd
    Database cross-references and differences (RAF-indexed):
    • PDB 6YKB (Start-341)
    Domains in SCOPe 2.08: d6ykba1, d6ykba2
  • Chain 'C':
    Compound: 5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase
    Species: Methanolacinia paynteri G-2000 [TaxId:694436]
    Gene: hmd
    Database cross-references and differences (RAF-indexed):
    • PDB 6YKB (Start-341)
    Domains in SCOPe 2.08: d6ykbc1, d6ykbc2
  • Heterogens: 5GP, FMT, GOL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6ykbA (A:)
mtikkvailgagcyrthsatgitnfaracevaemvgkpeiamthstiamaaelkylagid
nivisdpsfageftvvkdfdynevikahkenpetimpkirekvnelaktvpkppkgaihf
vhpedlglkvttddreavrdadliitwlpkgdmqkgiiekfagdikqgaiithactiptt
lfykifeelgiadkvevtsyhpgavpemkgqvyiaegyaseeaintiyelgkkarghafk
lpaeligpvcdmcaaltaityagllvyrdavmnilgapagfsqmmatesleqitaymkkv
giknleenldpgvflgtadsmnfgpiaeilptvlkslekrak

    Sequence, based on observed residues (ATOM records): (download) 
    >6ykbA (A:)
tikkvailgagcyrthsatgitnfaracevaemvgkpeiamthstiamaaelkylagidn
ivisdpsfageftvvkdfdynevikahkenpetimpkirekvnelaktvpkppkgaihfv
hpedlglkvttddreavrdadliitwlpkgdmqkgiiekfagdikqgaiithactipttl
fykifeelgiadkvevtsyhpgavpemkgqvyiaegyaseeaintiyelgkkarghafkl
paeligpvcdmcaaltaityagllvyrdavmnilgapagfsqmmatesleqitaymkkvg
iknleenldpgvflgtadsmnfgpiaeilptvlkslekrak

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6ykbC (C:)
mtikkvailgagcyrthsatgitnfaracevaemvgkpeiamthstiamaaelkylagid
nivisdpsfageftvvkdfdynevikahkenpetimpkirekvnelaktvpkppkgaihf
vhpedlglkvttddreavrdadliitwlpkgdmqkgiiekfagdikqgaiithactiptt
lfykifeelgiadkvevtsyhpgavpemkgqvyiaegyaseeaintiyelgkkarghafk
lpaeligpvcdmcaaltaityagllvyrdavmnilgapagfsqmmatesleqitaymkkv
giknleenldpgvflgtadsmnfgpiaeilptvlkslekrak

    Sequence, based on observed residues (ATOM records): (download) 
    >6ykbC (C:)
tikkvailgagcyrthsatgitnfaracevaemvgkpeiamthstiamaaelkylagidn
ivisdpsfageftvvkdfdynevikahkenpetimpkirekvnelaktvpkppkgaihfv
hpedlglkvttddreavrdadliitwlpkgdmqkgiiekfagdikqgaiithactipttl
fykifeelgiadkvevtsyhpgavpemkgqvyiaegyaseeaintiyelgkkarghafkl
paeligpvcdmcaaltaityagllvyrdavmnilgapagfsqmmatesleqitaymkkvg
iknleenldpgvflgtadsmnfgpiaeilptvlkslekrak