SCOPe 2.08: Structural Classification of Proteins

PDB entry 6vks

View 6vks on RCSB PDB site
Description: cryo-electron microscopy structures of a gonococcal multidrug efflux pump illuminate a mechanism of drug recognition with ampicillin
Deposited on 2020-01-22, released 2020-07-01
The last revision was dated 2020-08-05, with a file datestamp of 2020-07-31.
Experiment type: EM
Resolution: 3.02 Å
R-factor: N/A
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

Chain 'A':
Compound: Efflux pump membrane transporter
Species: NEISSERIA GONORRHOEAE [TaxId:485]
Gene: mtrD, E8M65_05860, E8M67_05810, E8M69_06545
Database cross-references and differences (RAF-indexed):
- Uniprot A0A4T9VBR9 (0-1048)
  - conflict (737)
  - conflict (773)
  - conflict (790)
  - conflict (793)
  - conflict (799)
  - conflict (806-807)
  - conflict (820)
  - conflict (822)
  - conflict (825)
  - conflict (838)
  - conflict (849)
  - conflict (853)
  - conflict (870-871)
  - conflict (874)
  - conflict (877-878)
  - conflict (898)
  - conflict (901)
  - conflict (906)
  - conflict (999)
Chain 'B':
Compound: Efflux pump membrane transporter
Species: NEISSERIA GONORRHOEAE [TaxId:485]
Gene: mtrD, E8M65_05860, E8M67_05810, E8M69_06545
Database cross-references and differences (RAF-indexed):
- Uniprot A0A4T9VBR9 (0-End)
  - conflict (737)
  - conflict (773)
  - conflict (790)
  - conflict (793)
  - conflict (799)
  - conflict (806-807)
  - conflict (820)
  - conflict (822)
  - conflict (825)
  - conflict (838)
  - conflict (849)
  - conflict (853)
  - conflict (870-871)
  - conflict (874)
  - conflict (877-878)
  - conflict (898)
  - conflict (901)
  - conflict (906)
  - conflict (999)
Chain 'C':
Compound: Efflux pump membrane transporter
Species: NEISSERIA GONORRHOEAE [TaxId:485]
Gene: mtrD, E8M65_05860, E8M67_05810, E8M69_06545
Database cross-references and differences (RAF-indexed):
- Uniprot A0A4T9VBR9 (0-End)
  - conflict (737)
  - conflict (773)
  - conflict (790)
  - conflict (793)
  - conflict (799)
  - conflict (806-807)
  - conflict (820)
  - conflict (822)
  - conflict (825)
  - conflict (838)
  - conflict (849)
  - conflict (853)
  - conflict (870-871)
  - conflict (874)
  - conflict (877-878)
  - conflict (898)
  - conflict (901)
  - conflict (906)
  - conflict (999)
Heterogens: AIX, PTY

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; same for both SEQRES and ATOM records:

>6vksA (A:)
makffidrpifawvisifiiaagifgikslpvsqypsvaaptitlhaiypgasaqvmegs
vlsviernmngvegldymstsadssgsgsvsltftpdtdenlaqvevqnklsevlstlpa
tvqqygvtvskarsnflmivmlssdvqsteemndyaqrnvvpelqriegvgqvrlfgaqr
amriwvdpkklqnynlsfadvgsalsaqniqisagsigslpavrgqtvtatvtaqgqlgt
aeefgnvilrantdgsniylkdvakvglgmedyssstrlngvnttgmavmlsnsgnamat
akavkerlavlekyfpqgmswktpydtskfveisiekvihtlieamvlvfvvmylflqni
rytliptivvpisllggfafisymgmsinvltmfamilvigivvddaivvvenverimag
eglppkeatkkamgqisgavigitavlisvfvplamfsgaagniykqfaltmassiafsa
flaltltpalcatmlktipkghheekkgffgwfnkkfdswthgyegrvakvlrktfrmmv
vyiglavvgvflfmrlptsflptedqgfvmvsvqlpagatkertdatlaqvtqlaksipe
ieniitvsgfsfsgsgqnmamgfailkdwnertasgsdavavagkltgmmmgtlkdgfgi
avvpppilelgngsglsinlqdrnntghtallakrneliqkmrasglfdpstvraggled
spqlkidinraaaaaqgvsfadirtalasalsssyvsdfpnqgrlqrvmvqadgdarmqp
adilnltvpnssgiavplssiatvswqmgteqsvrfngypamelsgspatgvstgqamea
vqkmvdelgsgyslewggqsreeakggsqtialyalaavavflvlaalyeswsiplavll
vmplglagaaagvtgrnlfegllgsvpsfandiyfqvgfvtvmglsaknailiiefakdl
qaqgksaveaaleaarlrfrpiimtsfafilgvvplyiaggassasqraigttvfwgmli
gtllsvflvplfyvvvrkffketahehem

Chain 'B':
Sequence, based on SEQRES records:

>6vksB (B:)
makffidrpifawvisifiiaagifgikslpvsqypsvaaptitlhaiypgasaqvmegs
vlsviernmngvegldymstsadssgsgsvsltftpdtdenlaqvevqnklsevlstlpa
tvqqygvtvskarsnflmivmlssdvqsteemndyaqrnvvpelqriegvgqvrlfgaqr
amriwvdpkklqnynlsfadvgsalsaqniqisagsigslpavrgqtvtatvtaqgqlgt
aeefgnvilrantdgsniylkdvakvglgmedyssstrlngvnttgmavmlsnsgnamat
akavkerlavlekyfpqgmswktpydtskfveisiekvihtlieamvlvfvvmylflqni
rytliptivvpisllggfafisymgmsinvltmfamilvigivvddaivvvenverimag
eglppkeatkkamgqisgavigitavlisvfvplamfsgaagniykqfaltmassiafsa
flaltltpalcatmlktipkghheekkgffgwfnkkfdswthgyegrvakvlrktfrmmv
vyiglavvgvflfmrlptsflptedqgfvmvsvqlpagatkertdatlaqvtqlaksipe
ieniitvsgfsfsgsgqnmamgfailkdwnertasgsdavavagkltgmmmgtlkdgfgi
avvpppilelgngsglsinlqdrnntghtallakrneliqkmrasglfdpstvraggled
spqlkidinraaaaaqgvsfadirtalasalsssyvsdfpnqgrlqrvmvqadgdarmqp
adilnltvpnssgiavplssiatvswqmgteqsvrfngypamelsgspatgvstgqamea
vqkmvdelgsgyslewggqsreeakggsqtialyalaavavflvlaalyeswsiplavll
vmplglagaaagvtgrnlfegllgsvpsfandiyfqvgfvtvmglsaknailiiefakdl
qaqgksaveaaleaarlrfrpiimtsfafilgvvplyiaggassasqraigttvfwgmli
gtllsvflvplfyvvvrkffketahehem

Sequence, based on observed residues (ATOM records):

>6vksB (B:)
makffidrpifawvisifiiaagifgikslpvsqypsvaaptitlhaiypgasaqvmegs
vlsviernmngvegldymstsadssgsgsvsltftpdtdenlaqvevqnklsevlstlpa
tvqqygvtvskarsnflmivmlssdvqsteemndyaqrnvvpelqriegvgqvrlfgaqr
amriwvdpkklqnynlsfadvgsalsaqniqisagsigslpavrgqtvtatvtaqgqlgt
aeefgnvilrantdgsniylkdvakvglgmedyssstrlngvnttgmavmlsnsgnamat
akavkerlavlekyfpqgmswktpydtskfveisiekvihtlieamvlvfvvmylflqni
rytliptivvpisllggfafisymgmsinvltmfamilvigivvddaivvvenverimag
eglppkeatkkamgqisgavigitavlisvfvplamfsgaagniykqfaltmassiafsa
flaltltpalcatmlktipkghheekkgffgwfnkkfdswthgyegrvakvlrktfrmmv
vyiglavvgvflfmrlptsflptedqgfvmvsvqlpagatkertdatlaqvtqlaksipe
ieniitvsgfsfsgsgqnmamgfailkdwnertasgsdavavagkltgmmmgtlkdgfgi
avvpppilelgngsglsinlqdrnntghtallakrneliqkmrasglfdpstvraggled
spqlkidinraaaaaqgvsfadirtalasalsssyvsdfpnqgrlqrvmvqadgdarmqp
adilnltvpnssgiavplssiatvswqmgteqsvrfngypamelsgspatgvstgqamea
vqkmvdelgsgyslewggqsreeakggsqtialyalaavavflvlaalyeswsiplavll
vmplglagaaagvtgrnlfegllgsvpsfandiyfqvgfvtvmglsaknailiiefakdl
qaqgksaveaaleaarlrfrpiimtsfafilgvvplyiaggassasqraigttvfwgmli
gtllsvflvplfyvvvrkff

Chain 'C':
Sequence, based on SEQRES records:

>6vksC (C:)
makffidrpifawvisifiiaagifgikslpvsqypsvaaptitlhaiypgasaqvmegs
vlsviernmngvegldymstsadssgsgsvsltftpdtdenlaqvevqnklsevlstlpa
tvqqygvtvskarsnflmivmlssdvqsteemndyaqrnvvpelqriegvgqvrlfgaqr
amriwvdpkklqnynlsfadvgsalsaqniqisagsigslpavrgqtvtatvtaqgqlgt
aeefgnvilrantdgsniylkdvakvglgmedyssstrlngvnttgmavmlsnsgnamat
akavkerlavlekyfpqgmswktpydtskfveisiekvihtlieamvlvfvvmylflqni
rytliptivvpisllggfafisymgmsinvltmfamilvigivvddaivvvenverimag
eglppkeatkkamgqisgavigitavlisvfvplamfsgaagniykqfaltmassiafsa
flaltltpalcatmlktipkghheekkgffgwfnkkfdswthgyegrvakvlrktfrmmv
vyiglavvgvflfmrlptsflptedqgfvmvsvqlpagatkertdatlaqvtqlaksipe
ieniitvsgfsfsgsgqnmamgfailkdwnertasgsdavavagkltgmmmgtlkdgfgi
avvpppilelgngsglsinlqdrnntghtallakrneliqkmrasglfdpstvraggled
spqlkidinraaaaaqgvsfadirtalasalsssyvsdfpnqgrlqrvmvqadgdarmqp
adilnltvpnssgiavplssiatvswqmgteqsvrfngypamelsgspatgvstgqamea
vqkmvdelgsgyslewggqsreeakggsqtialyalaavavflvlaalyeswsiplavll
vmplglagaaagvtgrnlfegllgsvpsfandiyfqvgfvtvmglsaknailiiefakdl
qaqgksaveaaleaarlrfrpiimtsfafilgvvplyiaggassasqraigttvfwgmli
gtllsvflvplfyvvvrkffketahehem

Sequence, based on observed residues (ATOM records):

>6vksC (C:)
makffidrpifawvisifiiaagifgikslpvsqypsvaaptitlhaiypgasaqvmegs
vlsviernmngvegldymstsadssgsgsvsltftpdtdenlaqvevqnklsevlstlpa
tvqqygvtvskarsnflmivmlssdvqsteemndyaqrnvvpelqriegvgqvrlfgaqr
amriwvdpkklqnynlsfadvgsalsaqniqisagsigslpavrgqtvtatvtaqgqlgt
aeefgnvilrantdgsniylkdvakvglgmedyssstrlngvnttgmavmlsnsgnamat
akavkerlavlekyfpqgmswktpydtskfveisiekvihtlieamvlvfvvmylflqni
rytliptivvpisllggfafisymgmsinvltmfamilvigivvddaivvvenverimag
eglppkeatkkamgqisgavigitavlisvfvplamfsgaagniykqfaltmassiafsa
flaltltpalcatmlktipkghheekkgffgwfnkkfdswthgyegrvakvlrktfrmmv
vyiglavvgvflfmrlptsflptedqgfvmvsvqlpagatkertdatlaqvtqlaksipe
ieniitvsgfsfsgsgqnmamgfailkdwnertasgsdavavagkltgmmmgtlkdgfgi
avvpppilelgngsglsinlqdrnntghtallakrneliqkmrasglfdpstvraggled
spqlkidinraaaaaqgvsfadirtalasalsssyvsdfpnqgrlqrvmvqadgdarmqp
adilnltvpnssgiavplssiatvswqmgteqsvrfngypamelsgspatgvstgqamea
vqkmvdelgsgyslewggqsreeakggsqtialyalaavavflvlaalyeswsiplavll
vmplglagaaagvtgrnlfegllgsvpsfandiyfqvgfvtvmglsaknailiiefakdl
qaqgksaveaaleaarlrfrpiimtsfafilgvvplyiaggassasqraigttvfwgmli
gtllsvflvplfyvvvrkffke