Structure Viewer: 6opa

>   Structure details

Crystal Structure of Bovine Fab Nc-Cow1 in complex with Hiv-1 Bg505 Sosip.664, and Human Fabs 35022 and Pgt128

PDB6opa
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution4.084Å
Number of Fvs3
In complexTrue
Light chain typeunknown,Lambda
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   F/I
Fv Details
Heavy chainF
Light chainI
Heavy subgroupunknown
Light subgroupunknown
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 73A 73B 73C 73D 73E 73F 73G 73H 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 101 102 103 104 105 106 107 108 109 110 111 112 113
E G Q L V Q S G A E L K K P G A S V K I S C K T S G Y R F N F Y H I N W I R Q T A G R G P E W M G W I S P Y S G D K N L A P A F Q D R V I M T T D T E V P V T S F T S T G A A Y M E I R N L K F D D T G T Y F C A K G L L R D G S S T W L P Y L W G Q G T L L 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 30A 30B 30C 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 95A 96 97 98 99 100 101 102 103 104 105 106 107
Q S V L T Q S A S V S G S L G Q S V T I S C T G P N S V C C S H K S I S W Y Q W P P G R A P T L I I Y E D N E R A P G I S P R F S G Y K S Y W S A Y L T I S D L R P E D E T T Y Y C C S Y T H N S G C V F G T G T K V S V L

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nameenvelope glycoprotein gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

CDR Sequences (chothia definition)
CDRH1GYRFNFY
CDRH2SPYSGD
CDRH3GLLRDGSSTWLPYL
CDRL1TGPNSVCCSHKSIS
CDRL2EDNERAP
CDRL3CSYTHNSGCV

Orientation Angles (from ABangle)
HL-62.35°
HC174.95°
HC2120.29°
LC1118.69°
LC286.61°
dc16.19Å
>   K/J
Fv Details
Heavy chainK
Light chainJ
Heavy subgroupunknown
Light subgroupIGLV2
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (imgt)

Heavy 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 31 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 60A 61 61A 61B 62 63 64 65 66 67 68 69 70 71 72 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 99 100 101 102 103 104 105 106 107 108 109 110 111 111A 111B 111C 111D 112 112A 112B 112C 112D 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128
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 N W Y 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 P K P W D 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 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 65 66 67 68 69 70 71 72 74 75 76 77 78 79 80 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127
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 chainsG
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG

CDR Sequences (imgt definition)
CDRH1GDSTAACNSF
CDRH2LSHCASYWNRGWT
CDRH3ARFGGEVLRYTDWPKPAWVDL
CDRL1SNNF
CDRL2DVN
CDRL3GSLVGNWDVI

Orientation Angles (from ABangle)
HL-58.72°
HC170.86°
HC2116.45°
LC1119.15°
LC283.05°
dc16.23Å
>   S/R
Fv Details
Heavy chainS
Light chainR
Heavy subgroupunknown
Light subgroupIGLV1
SpeciesHOMO SAPIENS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (imgt)

Heavy 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 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 63 64 65 66 67 68 69 70 71 72 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 99 100 101 102 103 104 105 106 107 108 109 110 111 111A 111B 111C 111D 111E 111F 111G 111H 111I 111J 111K 111L 111M 111N 111O 111P 111Q 111R 111S 111T 111U 111V 111W 111X 112 112A 112B 112C 112D 112E 112F 112G 112H 112I 112J 112K 112L 112M 112N 112O 112P 112Q 112R 112S 112T 112U 112V 112W 112X 112Y 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128
Q V Q L R E S G P S L M K P S Q T L S L T C T V S G S S L N D K S V G W V R Q A P G K A L Q W L G S V D T S G N T D Y N P G L K S R L S I T K D N S K S R I S L T V T G M T T E D S A T Y Y C I T A H Q K T N K K E C P E D Y T Y N P R C P Q Q Y G W S D C E Y T S R H I Y N S C G D Q R C Y G G F R D G M C D W Y V S A W G Q G L 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 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 65 66 67 68 69 70 71 72 74 75 76 77 78 79 80 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127
S Y E L T Q P S S V S G S L G Q R V S V T C S G S S S N V G N G Y V S W Y Q L I P G S A P R T I I Y G D T S R A S G V P E R F S G S R S G N T A T L T I S S L Q A E D E A D F F C A S P D D S S S N A V F G S G T T L T V L

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVG

CDR Sequences (imgt definition)
CDRH1GSSLNDKS
CDRH2VDTSGNT
CDRH3ITAHQKTNKKECPEDYTYNPRCPQQYGWSDCDCMGDRFGGYCRQDGCSNYIHRSTYEWYVSA
CDRL1SSNVGNGY
CDRL2GDT
CDRL3ASPDDSSSNAV

Orientation Angles (from ABangle)
HL-53.16°
HC174.65°
HC2120.86°
LC1120.01°
LC282.87°
dc15.65Å
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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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