Structure Viewer: 5c7k

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Crystal Structure Bg505 Sosip Gp140 Hiv-1 Env Trimer Bound to Broadly Neutralizing antibodies Pgt128 and 8anc195

PDB5c7k
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution4.6019Å
Number of Fvs2
In complexTrue
Light chain typeKappa,Lambda
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupunknown
Light subgroupIGLV2
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 31A 31B 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 52B 52C 52D 52E 52F 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E P Q L Q E S G P T L V E A S E T L S L T C A V S G D S T A A C N S F W G W V R Q P P G K G L E W V G S L S H C A S Y W N R G W T Y H N P S L K S R L T L A L D T P K N L V F L K L N S V T A A D T A T Y Y C A R F G G E V L R Y T D W P K P A W V D L W G R G T L V T V S S

Light chain

1 2 3 4 5 6 7 8 9 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 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 95A 96 97 98 99 100 101 102 103 104 105 106 107
Q S A L T Q P P S A S G S P G Q S I T I S C T G T S N N F V S W Y Q Q H A G K A P K L V I Y D V N K R P S G V P D R F S G S K S G N T A S L T V S G L Q T D D E A V Y Y C G S L V G N W D V I F G G G T K L T V L

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceRAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGSEKSGHHHHHH

CDR Sequences (chothia definition)
CDRH1GDSTAACNS
CDRH2SHCASYWNRGW
CDRH3FGGEVLRYTDWPKPAWVDL
CDRL1TGTSNNFVS
CDRL2DVNKRPS
CDRL3GSLVGNWDVI

Orientation Angles (from ABangle)
HL-57.71°
HC172.41°
HC2119.48°
LC1119.29°
LC286.72°
dc16.05Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupunknown
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 31A 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 71A 72 72A 72B 72C 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q I H L V Q S G T E V K K P G S S V T V S C K A Y G V N T F G L Y A V N W V R Q A P G Q S L E Y I G Q I W R W K S S A S H H F R G R V L I S A V D L T G S S P P I S S L E I K N L T S D D T A V Y F C T T T S T Y D K W S G L H H D G V M A F S S W G Q G T L I S V S A

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 30A 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 I G D T V R I S C R A S Q S I T G N W V A W Y Q Q R P G K A P R L L I Y R G A A L L G G V P S R F S G S A A G T D F T L T I G N L Q A E D F G T F Y C Q Q Y D T Y P G T F G Q G T K V E V K

Antigen Details
Antigen chainsC,D
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120; envelope glycoprotein gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD/RAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGSEKSGHHHHHH

CDR Sequences (chothia definition)
CDRH1GVNTFGLY
CDRH2WRWK
CDRH3TSTYDKWSGLHHDGVMAFSS
CDRL1RASQSITGNWVA
CDRL2RGAALLG
CDRL3QQYDTYPGT

Orientation Angles (from ABangle)
HL-64.88°
HC173.25°
HC2115.64°
LC1118.44°
LC283.24°
dc15.93Å
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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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