PDB entry 6jjo

View 6jjo on RCSB PDB site
Description: crystal structure of the degp dodecamer with a modulator
Deposited on 2019-02-26, released 2020-09-02
The last revision was dated 2020-10-14, with a file datestamp of 2020-10-09.
Experiment type: XRAY
Resolution: 4.16 Å
R-factor: N/A
AEROSPACI score: 0.09 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'B':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'C':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'D':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'E':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'F':
    Compound: periplasmic serine endoprotease degp
    Species: Escherichia coli K-12 [TaxId:83333]
    Gene: degP, htrA, ptd, b0161, JW0157
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0C0V0 (Start-468)
      • engineered mutation (230)
  • Chain 'G':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'H':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'I':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'J':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'K':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'L':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO
  • Chain 'M':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)
  • Chain 'N':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)
  • Chain 'O':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)
  • Chain 'P':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)
  • Chain 'Q':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)
  • Chain 'R':
    Compound: TMB-CYRKL modulator
    Species: Escherichia coli, synthetic [TaxId:562]
    Database cross-references and differences (RAF-indexed):
    • PDB 6JJO (0-4)

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6jjoA (A:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoA (A:)
aqqmpslapmlekvmpsvvsinveqkfmalgsgviidadkgyvvtnnhvvdnatvikvql
sdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglgetv
tsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggnig
igfaipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpns
saakagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqqs
fngiegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavkniaelrkvlds
kpsvlalniqrgdstiyllmq

  • Chain 'B':
    Sequence, based on SEQRES records:
    >6jjoB (B:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoB (B:)
qmpslapmlekvmpsvvsinvegstqkfmalgsgviidadkgyvvtnnhvvdnatvikvq
lsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglget
vtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggni
gigfaipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpn
ssaakagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqq
ssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavk
niaelrkvldskpsvlalniqrgdstiyllmq

  • Chain 'C':
    Sequence, based on SEQRES records:
    >6jjoC (C:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoC (C:)
qmpslapmlekvmpsvvsinvegstqkfmalgsgviidadkgyvvtnnhvvdnatvikvq
lsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglget
vtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggni
gigfaipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpn
ssaakagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqq
sfngiegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavkniaelrkvld
skpsvlalniqrgdstiyllmq

  • Chain 'D':
    Sequence, based on SEQRES records:
    >6jjoD (D:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoD (D:)
qmpslapmlekvmpsvvsinvegstqkfmalgsgviidadkgyvvtnnhvvdnatvikvq
lsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglget
vtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggni
gigfaipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpn
ssaakagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqq
svdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavkniae
lrkvldskpsvlalniqrgdstiyllmq

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6jjoE (E:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoE (E:)
qmpslapmlekvmpsvvsinvegstqkfmalgsgviidadkgyvvtnnhvvdnatvikvq
lsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglget
vtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggni
gigfaipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpn
ssaakagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqq
ssqsssifngiegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavkniae
lrkvldskpsvlalniqrgdstiyllmq

  • Chain 'F':
    Sequence, based on SEQRES records:
    >6jjoF (F:)
mgsshhhhhhssglvprgshmaetssattaqqmpslapmlekvmpsvvsinvegsttvnt
prmprnfqqffgddspfcqegspfqsspfcqggqggngggqqqkfmalgsgviidadkgy
vvtnnhvvdnatvikvqlsdgrkfdakmvgkdprsdialiqiqnpknltaikmadsdalr
vgdytvaignpfglgetvtsgivsalgrsglnaenyenfiqtdaainrgnaggalvnlng
eligintailapdggnigigfaipsnmvknltsqmveygqvkrgelgimgtelnselaka
mkvdaqrgafvsqvlpnssaakagikagdvitslngkpissfaalraqvgtmpvgskltl
gllrdgkqvnvnlelqqssqnqvdsssifngiegaemsnkgkdqgvvvnnvktgtpaaqi
glkkgdviiganqqavkniaelrkvldskpsvlalniqrgdstiyllmq

    Sequence, based on observed residues (ATOM records):
    >6jjoF (F:)
qmpslapmlekvmpsvvsinveqkfmalgsgviidadkgyvvtnnhvvdnatvikvqlsd
grkfdakmvgkdprsdialiqiqnpknltaikmadsdalrvgdytvaignpfglgetvts
givsalgrsglnaenyenfiqtdaainrgnaggalvnlngeligintailapdggnigig
faipsnmvknltsqmveygqvkrgelgimgtelnselakamkvdaqrgafvsqvlpnssa
akagikagdvitslngkpissfaalraqvgtmpvgskltlgllrdgkqvnvnlelqqsfn
giegaemsnkgkdqgvvvnnvktgtpaaqiglkkgdviiganqqavkniaelrkvldskp
svlalniqrgdstiyllmq

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoG (G:)
cyrkl

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoH (H:)
cyrkl

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoI (I:)
cyrkl

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoJ (J:)
cyrkl

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoK (K:)
cyrkl

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoL (L:)
cyrkl

  • Chain 'M':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoM (M:)
cyrkl

  • Chain 'N':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoN (N:)
cyrkl

  • Chain 'O':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoO (O:)
cyrkl

  • Chain 'P':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoP (P:)
cyrkl

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoQ (Q:)
cyrkl

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records:
    >6jjoR (R:)
cyrkl