PDB entry 4d9r

View 4d9r on RCSB PDB site
Description: Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D
Class: hydrolase/immune system
Keywords: Factor D, complement, antibody, exosite, Fab, chymotrypsin, protease, HYDROLASE-IMMUNE SYSTEM complex
Deposited on 2012-01-11, released 2012-02-22
The last revision prior to the SCOPe 2.08 freeze date was dated 2017-08-02, with a file datestamp of 2017-07-28.
Experiment type: XRAY
Resolution: 2.42 Å
R-factor: N/A
AEROSPACI score: 0.22 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: complement factor d
    Species: Homo sapiens [TaxId:9606]
    Gene: CFD, DF, Factor D, PFD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4d9ra_
  • Chain 'B':
    Compound: complement factor d
    Species: Homo sapiens [TaxId:9606]
    Gene: CFD, DF, Factor D, PFD
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d4d9rb_
  • Chain 'D':
    Compound: Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Gene: IGKC
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9R (0-103)
    • Uniprot P01834 (108-End)
      • linker (104-107)
    Domains in SCOPe 2.08: d4d9rd1, d4d9rd2
  • Chain 'E':
    Compound: Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Gene: IGHG1
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9R (0-109)
    • Uniprot P01857 (115-End)
      • linker (110-114)
    Domains in SCOPe 2.08: d4d9re_
  • Chain 'H':
    Compound: Fab heavy chain
    Species: Homo sapiens [TaxId:9606]
    Gene: IGHG1
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9R (0-109)
    • Uniprot P01857 (115-217)
      • linker (110-114)
    Domains in SCOPe 2.08: d4d9rh_
  • Chain 'L':
    Compound: Fab light chain
    Species: Homo sapiens [TaxId:9606]
    Gene: IGKC
    Database cross-references and differences (RAF-indexed):
    • PDB 4D9R (0-103)
    • Uniprot P01834 (108-213)
      • linker (104-107)
    Domains in SCOPe 2.08: d4d9rl1, d4d9rl2
  • Heterogens: CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9rA (A:)
ilggreaeaharpymasvqlngahlcggvlvaeqwvlsaahcledaadgkvqvllgahsl
sqpepskrlydvlravphpdsqpdtidhdllllqlsekatlgpavrplpwqrvdrdvapg
tlcdvagwgivnhagrrpdslqhvllpvldratcnrrthhdgaiterlmcaesnrrdsck
gdsggplvcggvlegvvtsgsrvcgnrkkpgiytrvasyaawidsvla

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9rB (B:)
ilggreaeaharpymasvqlngahlcggvlvaeqwvlsaahcledaadgkvqvllgahsl
sqpepskrlydvlravphpdsqpdtidhdllllqlsekatlgpavrplpwqrvdrdvapg
tlcdvagwgivnhagrrpdslqhvllpvldratcnrrthhdgaiterlmcaesnrrdsck
gdsggplvcggvlegvvtsgsrvcgnrkkpgiytrvasyaawidsvla

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >4d9rD (D:)
diqvtqspsslsasvgdrvtitcitstdidddmnwyqqkpgkvpkllisggntlrpgvps
rfsgsgsgtdftltisslqpedvatyyclqsdslpytfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9rD (D:)
diqvtqspsslsasvgdrvtitcitstdidddmnwyqqkpgkvpkllisggntlrpgvps
rfsgsgsgtdftltisslqpedvatyyclqsdslpytfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrge

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >4d9rE (E:)
evqlvqsgpelkkpgasvkvsckasgytftnygmnwvrqapgqglewmgwintytgetty
addfkgrfvfsldtsvstaylqisslkaedtavyycereggvnnwgqgtlvtvssastkg
psvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

    Sequence, based on observed residues (ATOM records): (download) 
    >4d9rE (E:)
evqlvqsgpelkkpgasvkvsckasgytftnygmnwvrqapgqglewmgwintytgetty
addfkgrfvfsldtsvstaylqisslkaedtavyycereggvnnwgqgtlvtvssastkg
psvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepk

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9rH (H:)
evqlvqsgpelkkpgasvkvsckasgytftnygmnwvrqapgqglewmgwintytgetty
addfkgrfvfsldtsvstaylqisslkaedtavyycereggvnnwgqgtlvtvssastkg
psvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglysl
ssvvtvpssslgtqtyicnvnhkpsntkvdkkvepksc

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >4d9rL (L:)
diqvtqspsslsasvgdrvtitcitstdidddmnwyqqkpgkvpkllisggntlrpgvps
rfsgsgsgtdftltisslqpedvatyyclqsdslpytfgqgtkveikrtvaapsvfifpp
sdeqlksgtasvvcllnnfypreakvqwkvdnalqsgnsqesvteqdskdstyslsstlt
lskadyekhkvyacevthqglsspvtksfnrgec