PDB entry 4ygd

View 4ygd on RCSB PDB site
Description: Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2
Class: protein transport
Keywords: beta-sandwich, ef-hand, cargo receptor, calcium binding, er, ergic, protein transport
Deposited on 2015-02-26, released 2016-04-06
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: 2.51 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Protein ERGIC-53
    Species: Homo sapiens [TaxId:9606]
    Gene: LMAN1, ERGIC53, F5F8D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ygda_
  • Chain 'B':
    Compound: multiple coagulation factor deficiency protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: MCFD2, SDNSF
    Database cross-references and differences (RAF-indexed):
  • Chain 'C':
    Compound: Protein ERGIC-53
    Species: Homo sapiens [TaxId:9606]
    Gene: LMAN1, ERGIC53, F5F8D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ygdc_
  • Chain 'D':
    Compound: multiple coagulation factor deficiency protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: MCFD2, SDNSF
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Protein ERGIC-53
    Species: Homo sapiens [TaxId:9606]
    Gene: LMAN1, ERGIC53, F5F8D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ygde_
  • Chain 'F':
    Compound: multiple coagulation factor deficiency protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: MCFD2, SDNSF
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: Protein ERGIC-53
    Species: Homo sapiens [TaxId:9606]
    Gene: LMAN1, ERGIC53, F5F8D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4ygdg_
  • Chain 'H':
    Compound: multiple coagulation factor deficiency protein 2
    Species: Homo sapiens [TaxId:9606]
    Gene: MCFD2, SDNSF
    Database cross-references and differences (RAF-indexed):
  • Heterogens: CA, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >4ygdA (A:)
mnhkvhmdgvggdpavalphrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirva
pslksqrgsvwtktkaafenwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadl
wngvgiffdsfdndgkknnpaiviignngqihydhqndgasqalascqrdfrnkpypvra
kityyqntltvminngftpdkndyefcakvenmiipaqghfgisaatggladdhdvlsfl
tfqlte

    Sequence, based on observed residues (ATOM records): (download) 
    >4ygdA (A:)
phrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirvapslksqrgsvwtktkaaf
enwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadlwngvgiffdsfdndgkkn
npaiviignngqihydhqndgasqalascqrdfrnkpypvrakityyqntltvminngft
pdkndyefcakvenmiipaqghfgisaatggladdhdvlsfltfqlt

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >4ygdC (C:)
mnhkvhmdgvggdpavalphrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirva
pslksqrgsvwtktkaafenwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadl
wngvgiffdsfdndgkknnpaiviignngqihydhqndgasqalascqrdfrnkpypvra
kityyqntltvminngftpdkndyefcakvenmiipaqghfgisaatggladdhdvlsfl
tfqlte

    Sequence, based on observed residues (ATOM records): (download) 
    >4ygdC (C:)
phrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirvapslksqrgsvwtktkaaf
enwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadlwngvgiffdsfdndgkkn
npaiviignngqihydhqndgasqalascqrdfrnkpypvrakityyqntltvminngft
pdkndyefcakvenmiipaqghfgisaatggladdhdvlsfltfqlt

  • Chain 'D':
    No sequence available.

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4ygdE (E:)
mnhkvhmdgvggdpavalphrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirva
pslksqrgsvwtktkaafenwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadl
wngvgiffdsfdndgkknnpaiviignngqihydhqndgasqalascqrdfrnkpypvra
kityyqntltvminngftpdkndyefcakvenmiipaqghfgisaatggladdhdvlsfl
tfqlte

    Sequence, based on observed residues (ATOM records): (download) 
    >4ygdE (E:)
phrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirvapslksqrgsvwtktkaaf
enwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadlwngvgiffdsfdndgkkn
npaiviignngqihydhqndgasqalascqrdfrnkpypvrakityyqntltvminngft
pdkndyefcakvenmiipaqghfgisaatggladdhdvlsfltfqlt

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >4ygdG (G:)
mnhkvhmdgvggdpavalphrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirva
pslksqrgsvwtktkaafenwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadl
wngvgiffdsfdndgkknnpaiviignngqihydhqndgasqalascqrdfrnkpypvra
kityyqntltvminngftpdkndyefcakvenmiipaqghfgisaatggladdhdvlsfl
tfqlte

    Sequence, based on observed residues (ATOM records): (download) 
    >4ygdG (G:)
phrrfeykysfkgphlvqsdgtvpfwahagnaipssdqirvapslksqrgsvwtktkaaf
enwevevtfrvtgrgrigadglaiwyaenqglegpvfgsadlwngvgiffdsfdndgkkn
npaiviignngqihydhqndgasqalascqrdfrnkpypvrakityyqntltvminngft
pdkndyefcakvenmiipaqghfgisaatggladdhdvlsfltfqlt

  • Chain 'H':
    No sequence available.