Structure Viewer: 5boz

>   Structure details

Ricin a Chain Bound to Camelid Nanobody (Vhh9)(E1)

PDB5boz
SpeciesLAMA GLAMA
MethodX-RAY DIFFRACTION
Resolution3.1Å
Number of Fvs6
In complexTrue
Light chain type
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   I/-
Fv Details
Heavy chainI
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   G/-
Fv Details
Heavy chainG
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   J/-
Fv Details
Heavy chainJ
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   L/-
Fv Details
Heavy chainL
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   H/-
Fv Details
Heavy chainH
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   K/-
Fv Details
Heavy chainK
Light chain
Heavy subgroupIGHV1
Light subgroup
SpeciesLAMA GLAMA
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 82A 82B 82C 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 101 102 103 104 105 106 107 108 109 110 111 112
Q V Q L V E S G G G L V Q A G G S L R L S C A A S G R T F S R S S M G W F R Q A P G K E R E F V A S I V W A D G T T L Y G D S V K G R F T V S R D N V K N M V Y L Q M N N L K P E D T A L Y Y C A D N K F V R G L V A V R A I D Y D Y W G Q G T Q V T V S

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namericin
Antigen speciesRICINUS COMMUNIS
Antigen sequenceKQYPIINFTTAGATVQSYTNFIRAVRGRLTTGADVRHEIPVLPNRVGLPINQRFILVELSNHAELSVTLALDVTNAYVVGYRAGNSAYFFHPDNQEDAEAITHLFTDVQNRYTFAFGGNYDRLEQLAGNLRENIELGNGPLEEAISALYYYSTGGTQLPTLARSFIICIQMISEAARFQYIEGEMRTRIRYNRRSAPDPSVITLENSWGRLSTAIQESNQGAFASPIQLQRRNGSKFSVYDVSILIPIIALMVYRCAPPPS

CDR Sequences (chothia definition)
CDRH1GRTFSRS
CDRH2VWADGT
CDRH3NKFVRGLVAVRAIDYDY

>   Downloads

Additional links and files for download: see help for more details.

Chothia-numbered structure Download
IMGT-numbered structure Download
Non-annotated structure from the PDB Download
Summary file for this antibody Download

Schneider, C., Raybould, M.I.J., Deane, C.M. (2022) SAbDab in the Age of Biotherapeutics: Updates including SAbDab-Nano, the Nanobody Structure Tracker. Nucleic Acids Res. 50(D1):D1368-D1372 [link]

SAbDab paper: Dunbar, J., Krawczyk, K. et al (2014). Nucleic Acids Res. 42. D1140-D1146 [link]

Thera-SAbDab paper: Raybould, M.I.J., Marks, C. et al (2019). Nucleic Acids Res. gkz827 [link]

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