PDB entry 6yc4

View 6yc4 on RCSB PDB site
Description: Crystal structure of the steady-state activated state of the light-driven sodium pump KR2 in the pentameric form at room temperature, pH 8.0
Class: membrane protein
Keywords: rhodopsin, ion pumping, retinal, sodium pump, intermediate state, MEMBRANE PROTEIN
Deposited on 2020-03-18, released 2020-04-08
The last revision prior to the SCOPe 2.08 freeze date was dated 2020-05-13, with a file datestamp of 2020-05-08.
Experiment type: XRAY
Resolution: 2.6 Å
R-factor: N/A
AEROSPACI score: 0.2 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Sodium pumping rhodopsin
    Species: Dokdonia eikasta [TaxId:308116]
    Gene: NaR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yc4a_
  • Chain 'B':
    Compound: Sodium pumping rhodopsin
    Species: Dokdonia eikasta [TaxId:308116]
    Gene: NaR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yc4b_
  • Chain 'C':
    Compound: Sodium pumping rhodopsin
    Species: Dokdonia eikasta [TaxId:308116]
    Gene: NaR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yc4c_
  • Chain 'D':
    Compound: Sodium pumping rhodopsin
    Species: Dokdonia eikasta [TaxId:308116]
    Gene: NaR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yc4d_
  • Chain 'E':
    Compound: Sodium pumping rhodopsin
    Species: Dokdonia eikasta [TaxId:308116]
    Gene: NaR
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d6yc4e_
  • Heterogens: NA, OLC, LFA, RET, GOL, OLA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6yc4A (A:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsknkel

    Sequence, based on observed residues (ATOM records): (download) 
    >6yc4A (A:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsk

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6yc4B (B:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsknkel

    Sequence, based on observed residues (ATOM records): (download) 
    >6yc4B (B:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsk

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >6yc4C (C:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsknkel

    Sequence, based on observed residues (ATOM records): (download) 
    >6yc4C (C:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsk

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >6yc4D (D:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsknkel

    Sequence, based on observed residues (ATOM records): (download) 
    >6yc4D (D:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsk

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6yc4E (E:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsknkel

    Sequence, based on observed residues (ATOM records): (download) 
    >6yc4E (E:)
qelgnanfenfigategfseiayqftshiltlgyavmlagllyfiltiknvdkkfqmsni
lsavvmvsaflllyaqaqnwtssftfneevgryfldpsgdlfnngyrylnwlidvpmllf
qilfvvslttskfssvrnqfwfsgammiitgyigqfyevsnltaflvwgaissafffhil
wvmkkvinegkegispagqkilsniwilfliswtlypgaylmpyltgvdgflysedgvma
rqlvytiadvsskviygvllgnlaitlsk