PDB entry 7kdu

View 7kdu on RCSB PDB site
Description: Ricin bound to VHH antibody V5E4
Class: toxin
Keywords: Ribosome inactivating protein, TOXIN
Deposited on 2020-10-09, released 2021-08-04
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-08-04, with a file datestamp of 2021-07-30.
Experiment type: XRAY
Resolution: 2.81 Å
R-factor: N/A
AEROSPACI score: 0.21 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Ricin chain A
    Species: Ricinus communis [TaxId:3988]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7kdua_
  • Chain 'B':
    Compound: Ricin chain B
    Species: Ricinus communis [TaxId:3988]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d7kdub1, d7kdub2
  • Chain 'C':
    Compound: VHH antibody V5E4
    Species: Vicugna pacos [TaxId:30538]
    Database cross-references and differences (RAF-indexed):
    • PDB 7KDU (0-132)
    Domains in SCOPe 2.08: d7kduc_
  • Heterogens: EDO, ZN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >7kduA (A:)
ifpkqypiinfttagatvqsytnfiravrgrlttgadvrheipvlpnrvglpinqrfilv
elsnhaelsvtlaldvtnayvvgyragnsayffhpdnqedaeaithlftdvqnrytfafg
gnydrleqlagnlrenielgngpleeaisalyyystggtqlptlarsfiiciqmiseaar
fqyiegemrtrirynrrsapdpsvitlenswgrlstaiqesnqgafaspiqlqrrngskf
svydvsilipiialmvyrcapppssqf

    Sequence, based on observed residues (ATOM records): (download) 
    >7kduA (A:)
ypiinfttagatvqsytnfiravrgrlttgadvrheipvlpnrvglpinqrfilvelsnh
aelsvtlaldvtnayvvgyragnsayffhpdnqedaeaithlftdvqnrytfafggnydr
leqlagnlrenielgngpleeaisalyyystggtqlptlarsfiiciqmiseaarfqyie
gemrtrirynrrsapdpsvitlenswgrlstaiqesnqgafaspiqlqrrngskfsvydv
silipiialmvyrcap

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >7kduB (B:)
advcmdpepivrivgrnglcvdvrdgrfhngnaiqlwpcksntdanqlwtlkrdntirsn
gkclttygyspgvyvmiydcntaatdatrwqiwdngtiinprsslvlaatsgnsgttltv
qtniyavsqgwlptnntqpfvttivglyglclqansgqvwiedcssekaeqqwalyadgs
irpqqnrdncltsdsniretvvkilscgpassgqrwmfkndgtilnlysglvldvrasdp
slkqiilyplhgdpnqiwlplf

    Sequence, based on observed residues (ATOM records): (download) 
    >7kduB (B:)
vcmdpepivrivgrnglcvdvrdgrfhngnaiqlwpcksntdanqlwtlkrdntirsngk
clttygyspgvyvmiydcntaatdatrwqiwdngtiinprsslvlaatsgnsgttltvqt
niyavsqgwlptnntqpfvttivglyglclqansgqvwiedcsseqqwalyadgsirpqq
nrdncltsdsniretvvkilscgpassgqrwmfkndgtilnlysglvldvrasdpslkqi
ilyplhgdpnqiwlplf

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >7kduC (C:)
naqvqlvetggglvqaggslrlscvasggtfssyamgwfrqapgkerdfvagislsgagt
yyqdsvkgrftisrdnakntvylqmnslkpedtavyyckatgergygdqgylevwgrgtl
vtvssepktpkpq

    Sequence, based on observed residues (ATOM records): (download) 
    >7kduC (C:)
naqvqlvetgrlscvasgtfssyamgwfrapkerdfvaislsgatyyqdsvkgrftisrd
nantvylqmnspedtavyyckatgergyqgylevwgrt