PDB entry 6nmr

View 6nmr on RCSB PDB site
Description: Blocking Fab 119 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1
Class: immune system
Keywords: SIRP-alpha, Signal regulatory protein alpha, Signal-regulatory protein alpha, Tyrosine-protein phosphatase non-receptor type substrate 1, CD47, Cluster of Differentiation 47, anti-SIRP-alpha antibody, Blocking anti-SIRP-alpha antibody, Non-Blocking anti-SIRP-alpha antibody, Kick-Off anti-SIRP-alpha antibody, anti-SIRP-alpha antibody in complex with SIRP-alpha, IMMUNE SYSTEM
Deposited on 2019-01-11, released 2019-08-07
The last revision prior to the SCOPe 2.08 freeze date was dated 2019-08-14, with a file datestamp of 2019-08-09.
Experiment type: XRAY
Resolution: 2.42 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR
    Domains in SCOPe 2.08: d6nmra_
  • Chain 'B':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrb1, d6nmrb2
  • Chain 'E':
    Compound: tyrosine-protein phosphatase non-receptor type substrate 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP
    Database cross-references and differences (RAF-indexed):
    • Uniprot P78324
      • conflict (79)
    Domains in SCOPe 2.08: d6nmre_
  • Chain 'F':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrf_
  • Chain 'G':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrg1, d6nmrg2
  • Chain 'H':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrh_
  • Chain 'I':
    Compound: tyrosine-protein phosphatase non-receptor type substrate 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP
    Database cross-references and differences (RAF-indexed):
    • Uniprot P78324
      • conflict (79)
    Domains in SCOPe 2.08: d6nmri_
  • Chain 'J':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrj_
  • Chain 'K':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrk1, d6nmrk2
  • Chain 'L':
    Compound: Fab 119 anti-SIRP-alpha antibody Variable Light Chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6NMR (0-End)
    Domains in SCOPe 2.08: d6nmrl1, d6nmrl2
  • Chain 'M':
    Compound: tyrosine-protein phosphatase non-receptor type substrate 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP
    Database cross-references and differences (RAF-indexed):
    • Uniprot P78324
      • conflict (79)
    Domains in SCOPe 2.08: d6nmrm_
  • Chain 'S':
    Compound: tyrosine-protein phosphatase non-receptor type substrate 1
    Species: Homo sapiens [TaxId:9606]
    Gene: SIRPA, BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP
    Database cross-references and differences (RAF-indexed):
    • Uniprot P78324
      • conflict (79)
    Domains in SCOPe 2.08: d6nmrs_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >6nmrA (A:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkschhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrA (A:)
vqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyads
vkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvssa
stkgpsvfplapsskgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepks

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >6nmrB (B:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrB (B:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrg

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >6nmrE (E:)
eeelqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprv
ttvsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsvrakpst
rhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrE (E:)
eelqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprvt
tvsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtels

  • Chain 'F':
    Sequence, based on SEQRES records: (download) 
    >6nmrF (F:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkschhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrF (F:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapssgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvep

  • Chain 'G':
    Sequence, based on SEQRES records: (download) 
    >6nmrG (G:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrG (G:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'H':
    Sequence, based on SEQRES records: (download) 
    >6nmrH (H:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkschhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrH (H:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapssksgtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >6nmrI (I:)
eeelqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprv
ttvsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsvrakpst
rhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrI (I:)
elqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprvtt
vsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsv

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >6nmrJ (J:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqss
glyslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkschhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrJ (J:)
dvqllesgggvvqpggslrlscaasgfsfsnfamtwvrqapgeglewvstigsgdtyyad
svkgrftisrdnskntlylqmnslraedtavyycakdstvswsgdffdywgqgtlvtvss
astkgpsvfplapsssggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssgly
slssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'K':
    Sequence, based on SEQRES records: (download) 
    >6nmrK (K:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrK (K:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrg

  • Chain 'L':
    Sequence, based on SEQRES records: (download) 
    >6nmrL (L:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrL (L:)
eivltqspatlsvspgeratfscrasqnvkndlawyqqrpgqaprlliyaariretgipe
rfsgsgsgteftltitslqsedfavyycqqyydwppftfgggtkveikrtvaapsvfifp
psdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstl
tlskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'M':
    Sequence, based on SEQRES records: (download) 
    >6nmrM (M:)
eeelqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprv
ttvsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsvrakpst
rhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrM (M:)
elqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprvtt
vsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsv

  • Chain 'S':
    Sequence, based on SEQRES records: (download) 
    >6nmrS (S:)
eeelqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprv
ttvsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsvrakpst
rhhhhhh

    Sequence, based on observed residues (ATOM records): (download) 
    >6nmrS (S:)
elqviqpdksvlvaagetatlrctatslipvgpiqwfrgagpgreliynqkeghfprvtt
vsdltkrnnmdfsirigaitpadagtyycvkfrkgspddvefksgagtelsvr