PDB entry 2ak4

View 2ak4 on RCSB PDB site
Description: Crystal Structure of SB27 TCR in complex with HLA-B*3508-13mer peptide
Class: immune system
Keywords: T cell receptor, bulged epitopes, pMHC/TCR complex, IMMUNE SYSTEM
Deposited on 2005-08-03, released 2005-10-11
The last revision prior to the SCOPe 2.01 freeze date was dated 2009-02-24, with a file datestamp of 2009-03-01.
Experiment type: XRAY
Resolution: 2.5 Å
R-factor: 0.247
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: HLA-B35 variant
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • GB CAA80366 (0-275)
    Domains in SCOPe 2.01: d2ak4a1, d2ak4a2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2ak4b_
  • Chain 'C':
    Compound: EBV peptide LPEPLPQGQLTAY
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (0-12)
  • Chain 'D':
    Compound: SB27 T cell receptor alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4
    Domains in SCOPe 2.01: d2ak4d1, d2ak4d2
  • Chain 'E':
    Compound: SB27 T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (Start-244)
    Domains in SCOPe 2.01: d2ak4e1, d2ak4e2
  • Chain 'F':
    Compound: HLA-B35 variant
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • GB CAA80366 (0-275)
    Domains in SCOPe 2.01: d2ak4f1, d2ak4f2
  • Chain 'G':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2ak4g_
  • Chain 'H':
    Compound: EBV peptide LPEPLPQGQLTAY
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (0-12)
  • Chain 'I':
    Compound: SB27 T cell receptor alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4
    Domains in SCOPe 2.01: d2ak4i1, d2ak4i2
  • Chain 'J':
    Compound: SB27 T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (Start-244)
    Domains in SCOPe 2.01: d2ak4j1, d2ak4j2
  • Chain 'K':
    Compound: HLA-B35 variant
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • GB CAA80366 (0-275)
    Domains in SCOPe 2.01: d2ak4k1, d2ak4k2
  • Chain 'L':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2ak4l_
  • Chain 'M':
    Compound: EBV peptide LPEPLPQGQLTAY
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (0-12)
  • Chain 'N':
    Compound: SB27 T cell receptor alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4
    Domains in SCOPe 2.01: d2ak4n1, d2ak4n2
  • Chain 'P':
    Compound: SB27 T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (Start-244)
    Domains in SCOPe 2.01: d2ak4p1, d2ak4p2
  • Chain 'Q':
    Compound: HLA-B35 variant
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • GB CAA80366 (0-275)
    Domains in SCOPe 2.01: d2ak4q1, d2ak4q2
  • Chain 'R':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d2ak4r_
  • Chain 'S':
    Compound: EBV peptide LPEPLPQGQLTAY
    Species: synthetic, synthetic
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (0-12)
  • Chain 'T':
    Compound: SB27 T cell receptor alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4
    Domains in SCOPe 2.01: d2ak4t1, d2ak4t2
  • Chain 'U':
    Compound: SB27 T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 2AK4 (Start-244)
    Domains in SCOPe 2.01: d2ak4u1, d2ak4u2
  • Heterogens: IOD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4A (A:)
gshsmryfytamsrpgrgeprfiavgyvddtqfvrfdsdaasprteprapwieqegpeyw
drntqifktntqtyreslrnlrgyynqseagshiiqrmygcdlgpdgrllrghdqsaydg
kdyialnedlsswtaadtaaqitqrkweaarvaeqrrayleglcvewlrrylengketlq
radppkthvthhpvsdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdrt
fqkwaavvvpsgeeqrytchvqheglpkpltlrwep

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4B (B:)
iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2ak4D (D:)
hmaqkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqn
eisgryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniq
npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
awsnksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4D (D:)
qkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqneis
gryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffps

  • Chain 'E':
    Sequence, based on SEQRES records: (download) 
    >2ak4E (E:)
hmnagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkg
evpngynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4E (E:)
gvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevpn
gynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlknvfpp
evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
d

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4F (F:)
gshsmryfytamsrpgrgeprfiavgyvddtqfvrfdsdaasprteprapwieqegpeyw
drntqifktntqtyreslrnlrgyynqseagshiiqrmygcdlgpdgrllrghdqsaydg
kdyialnedlsswtaadtaaqitqrkweaarvaeqrrayleglcvewlrrylengketlq
radppkthvthhpvsdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdrt
fqkwaavvvpsgeeqrytchvqheglpkpltlrwep

  • Chain 'G':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4G (G:)
iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    Sequence, based on SEQRES records: (download) 
    >2ak4I (I:)
hmaqkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqn
eisgryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniq
npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
awsnksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4I (I:)
qkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqneis
gryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffps

  • Chain 'J':
    Sequence, based on SEQRES records: (download) 
    >2ak4J (J:)
hmnagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkg
evpngynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4J (J:)
gvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevpn
gynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlknvfpp
evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
d

  • Chain 'K':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4K (K:)
gshsmryfytamsrpgrgeprfiavgyvddtqfvrfdsdaasprteprapwieqegpeyw
drntqifktntqtyreslrnlrgyynqseagshiiqrmygcdlgpdgrllrghdqsaydg
kdyialnedlsswtaadtaaqitqrkweaarvaeqrrayleglcvewlrrylengketlq
radppkthvthhpvsdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdrt
fqkwaavvvpsgeeqrytchvqheglpkpltlrwep

  • Chain 'L':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4L (L:)
iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm

  • Chain 'M':
    No sequence available.

  • Chain 'N':
    Sequence, based on SEQRES records: (download) 
    >2ak4N (N:)
hmaqkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqn
eisgryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniq
npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
awsnksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4N (N:)
qkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqneis
gryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffps

  • Chain 'P':
    Sequence, based on SEQRES records: (download) 
    >2ak4P (P:)
hmnagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkg
evpngynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4P (P:)
gvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevpn
gynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlknvfpp
evavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
ndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
d

  • Chain 'Q':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4Q (Q:)
gshsmryfytamsrpgrgeprfiavgyvddtqfvrfdsdaasprteprapwieqegpeyw
drntqifktntqtyreslrnlrgyynqseagshiiqrmygcdlgpdgrllrghdqsaydg
kdyialnedlsswtaadtaaqitqrkweaarvaeqrrayleglcvewlrrylengketlq
radppkthvthhpvsdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdrt
fqkwaavvvpsgeeqrytchvqheglpkpltlrwep

  • Chain 'R':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ak4R (R:)
iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm

  • Chain 'S':
    No sequence available.

  • Chain 'T':
    Sequence, based on SEQRES records: (download) 
    >2ak4T (T:)
hmaqkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqn
eisgryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniq
npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
awsnksdfacanafnnsiipedtffpspess

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4T (T:)
qkvtqaqteisvvekedvtldcvyetrdttyylfwykqppsgelvflirrnsfdeqneis
gryswnfqkstssfnftitasqvvdsavyfcalsgfyntdklifgtgtrlqvfpniqnpd
pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
nksdfacanafnnsiipedtffps

  • Chain 'U':
    Sequence, based on SEQRES records: (download) 
    >2ak4U (U:)
hmnagvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkg
evpngynvsrlnkrefslrlesaapsqtsvyfcaspglageyeqyfgpgtrltvtedlkn
vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
wgrad

    Sequence, based on observed residues (ATOM records): (download) 
    >2ak4U (U:)
gvtqtpkfqvlktgqsmtlqcaqdmnhnsmywyrqdpgmglrliyysasegttdkgevpn
gynvsrlnkrefslrlesaapsqtsvyfcaspglaeqyfgpgtrltvtedlknvfppeva
vfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpalnds
ryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgrad