Structure Viewer: 2qad

>   Structure details

Structure of Tyrosine-Sulfated 412D antibody complexed with Hiv-1 Yu2 Gp120 and Cd4

PDB2qad
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.3Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   D/C
Fv Details
Heavy chainD
Light chainC
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 101 102 103 104 105 106 107 108 109 110 111 112
E V Q L V Q S G A E V K K P G S S V K V S C K A S G G T F S N Y A I N W V R Q A P G Q G L E W M G G I I P I F N I A H Y A Q R F Q G R V S I T A D E S T S T A Y M E L S S L R S E D T A V F Y C A S P Y P N D Y N D Y A P E E G M S W Y F D L W G R G T L V T V 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
D I Q M T Q S P S T L S A S V G D R V T I T C R A S Q S I S N W L A W Y Q Q K P G R A P K L L M Y K A S S L K S G V P S R F S G S G S G T E F T L T I S S L Q S D D F A T Y Y C Q Q H D S S P Y T F G Q G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGTFSNY
CDRH2IPIFNI
CDRH3PYPNDYNDYAPEEGMSWYFDL
CDRL1RASQSISNWLA
CDRL2KASSLKS
CDRL3QQHDSSPYT

Orientation Angles (from ABangle)
HL-55.84°
HC172.37°
HC2114.92°
LC1122.07°
LC283.6°
dc16.55Å
>   H/G
Fv Details
Heavy chainH
Light chainG
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 101 102 103 104 105 106 107 108 109 110 111 112
E V Q L V Q S G A E V K K P G S S V K V S C K A S G G T F S N Y A I N W V R Q A P G Q G L E W M G G I I P I F N I A H Y A Q R F Q G R V S I T A D E S T S T A Y M E L S S L R S E D T A V F Y C A S P Y P N D Y N D Y A P E E G M S W Y F D L W G R G T L V T V 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
D I Q M T Q S P S T L S A S V G D R V T I T C R A S Q S I S N W L A W Y Q Q K P G R A P K L L M Y K A S S L K S G V P S R F S G S G S G T E F T L T I S S L Q S D D F A T Y Y C Q Q H D S S P Y T F G Q G T K L E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRALYTTGEIIGDIRQAHCNLSKTQWENTLEQIAIKLKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGTFSNY
CDRH2IPIFNI
CDRH3PYPNDYNDYAPEEGMSWYFDL
CDRL1RASQSISNWLA
CDRL2KASSLKS
CDRL3QQHDSSPYT

Orientation Angles (from ABangle)
HL-56.13°
HC172.22°
HC2114.97°
LC1122.08°
LC283.2°
dc16.5Å
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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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