Structure Viewer: 5kaq

>   Structure details

Crystal Structure of Broadly Neutralizing influenza a antibody 31.a.83 in complex with Hemagglutinin Hong Kong 1968.

PDB5kaq
SpeciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
MethodX-RAY DIFFRACTION
Resolution3.514Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   F/G
Fv Details
Heavy chainF
Light chainG
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
In complex?True
scFv?False
Has constant domain?True

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 100J 100K 100L 100M 100N 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V Q P G E S L R V S C A A S G F T F R D S A L S W V R Q A P G K G L E W V S A I S G N G G A T Y Y A D T V K G R F T I S R D N S Q T T L Y L Q M N S L R A D D T A T Y Y C A K D E S P P I Y N L M P G Y Y S T Y Y Y M D V W G K G T T V T V S S

Light 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 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 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
E I V M T Q S P V T L S V S P G E T A T L S C R A S Q S V R S N L A W Y Q Q K P G Q A P R L L I Y G A S T R A T D I P A R F S G S G S G T E F T L S I S S L Q S D D F A V Y Y C Q Q Y N H W L R T F G Q G T K L E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namehemagglutinin
Antigen speciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
Antigen sequenceQDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGVSGRLVPR

CDR Sequences (chothia definition)
CDRH1GFTFRDS
CDRH2SGNGGA
CDRH3DESPPIYNLMPGYYSTYYYMDV
CDRL1RASQSVRSNLA
CDRL2GASTRAT
CDRL3QQYNHWLRT

Orientation Angles (from ABangle)
HL-59.03°
HC171.5°
HC2121.5°
LC1120.63°
LC283.06°
dc16.17Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
In complex?True
scFv?False
Has constant domain?True

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 100J 100K 100L 100M 100N 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V Q P G E S L R V S C A A S G F T F R D S A L S W V R Q A P G K G L E W V S A I S G N G G A T Y Y A D T V K G R F T I S R D N S Q T T L Y L Q M N S L R A D D T A T Y Y C A K D E S P P I Y N L M P G Y Y S T Y Y Y M D V W G K G T T V T V S S

Light 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 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 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
E I V M T Q S P V T L S V S P G E T A T L S C R A S Q S V R S N L A W Y Q Q K P G Q A P R L L I Y G A S T R A T D I P A R F S G S G S G T E F T L S I S S L Q S D D F A V Y Y C Q Q Y N H W L R T F G Q G T K L E I K

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namehemagglutinin
Antigen speciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
Antigen sequenceQDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGVSGRLVPR

CDR Sequences (chothia definition)
CDRH1GFTFRDS
CDRH2SGNGGA
CDRH3DESPPIYNLMPGYYSTYYYMDV
CDRL1RASQSVRSNLA
CDRL2GASTRAT
CDRL3QQYNHWLRT

Orientation Angles (from ABangle)
HL-58.52°
HC172.54°
HC2120.23°
LC1118.59°
LC282.64°
dc15.93Å
>   Q/R
Fv Details
Heavy chainQ
Light chainR
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
In complex?True
scFv?False
Has constant domain?True

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 100J 100K 100L 100M 100N 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L L E S G G G L V Q P G E S L R V S C A A S G F T F R D S A L S W V R Q A P G K G L E W V S A I S G N G G A T Y Y A D T V K G R F T I S R D N S Q T T L Y L Q M N S L R A D D T A T Y Y C A K D E S P P I Y N L M P G Y Y S T Y Y Y M D V W G K G T T V T V S S

Light 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 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 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107
E I V M T Q S P V T L S V S P G E T A T L S C R A S Q S V R S N L A W Y Q Q K P G Q A P R L L I Y G A S T R A T D I P A R F S G S G S G T E F T L S I S S L Q S D D F A V Y Y C Q Q Y N H W L R T F G Q G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namehemagglutinin
Antigen speciesINFLUENZA A VIRUS (A/HONG KONG/1-4-MA21-1/1968(H3N2))
Antigen sequenceQDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIESRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGVSGRLVPR

CDR Sequences (chothia definition)
CDRH1GFTFRDS
CDRH2SGNGGA
CDRH3DESPPIYNLMPGYYSTYYYMDV
CDRL1RASQSVRSNLA
CDRL2GASTRAT
CDRL3QQYNHWLRT

Orientation Angles (from ABangle)
HL-58.84°
HC173.29°
HC2121.8°
LC1119.77°
LC282.94°
dc15.66Å
>   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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