Structure Viewer: 9ber

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Cryo-Em Structure of the Hiv-1 Jr-Fl Idl Env Trimer in complex with Pgt122 Fab

PDB9ber
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution4.1Å
Number of Fvs3
In complexTrue
Light chain typeLambda
Has constant regionFalse
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>   Fv information

This PDB has 3 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 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 100O 100P 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V H L Q E S G P G L V K P S E T L S L T C N V S G T L V R D N Y W S W I R Q P L G K Q P E W I G Y V H D S G D T N Y N P S L K S R V H L S L D K S K N L V S L R L T G V T A A D S A I Y Y C A T T K H G R R I Y G V V A F K E W F T Y F Y M D V W G K G T S V T V S S

Light chain

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 68A 68B 68C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
V S V A P G Q T A R I T C G E E S L G S R S V I W Y Q Q R P G Q A P S L I I Y N N N D R P S G I P D R F S G S P G S T F G T T A T L T I T S V E A G D E A D Y Y C H I W D S R R P T N W V F G E G T T L I V L

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWCQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNITTSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCNTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGTGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGGCGAMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GTLVRDN
CDRH2HDSGD
CDRH3TKHGRRIYGVVAFKEWFTYFYMDV
CDRL1GEESLGSRSVI
CDRL2NNNDRPS
CDRL3HIWDSRRPTNWV

Orientation Angles (from ABangle)
HL-63.5°
HC178.12°
HC2120.94°
LC1117.12°
LC288.06°
dc17.21Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV4
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 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 100O 100P 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V H L Q E S G P G L V K P S E T L S L T C N V S G T L V R D N Y W S W I R Q P L G K Q P E W I G Y V H D S G D T N Y N P S L K S R V H L S L D K S K N L V S L R L T G V T A A D S A I Y Y C A T T K H G R R I Y G V V A F K E W F T Y F Y M D V W G K G T S V T V S S

Light chain

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 68A 68B 68C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
V S V A P G Q T A R I T C G E E S L G S R S V I W Y Q Q R P G Q A P S L I I Y N N N D R P S G I P D R F S G S P G S T F G T T A T L T I T S V E A G D E A D Y Y C H I W D S R R P T N W V F G E G T T L I V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWCQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNITTSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCNTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGTGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGGCGAMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GTLVRDN
CDRH2HDSGD
CDRH3TKHGRRIYGVVAFKEWFTYFYMDV
CDRL1GEESLGSRSVI
CDRL2NNNDRPS
CDRL3HIWDSRRPTNWV

Orientation Angles (from ABangle)
HL-61.8°
HC180.31°
HC2122.49°
LC1118.33°
LC289.77°
dc17.0Å
>   J/K
Fv Details
Heavy chainJ
Light chainK
Heavy subgroupIGHV4
Light subgroupIGLV3
SpeciesHOMO SAPIENS
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 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 100O 100P 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V H L Q E S G P G L V K P S E T L S L T C N V S G T L V R D N Y W S W I R Q P L G K Q P E W I G Y V H D S G D T N Y N P S L K S R V H L S L D K S K N L V S L R L T G V T A A D S A I Y Y C A T T K H G R R I Y G V V A F K E W F T Y F Y M D V W G K G T S V T V S S

Light chain

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 68A 68B 68C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
V S V A P G Q T A R I T C G E E S L G S R S V I W Y Q Q R P G Q A P S L I I Y N N N D R P S G I P D R F S G S P G S T F G T T A T L T I T S V E A G D E A D Y Y C H I W D S R R P T N W V F G E G T T L I V L

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVEKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEVVLENVTEHFNMWKNNMVEQMQEDIISLWCQSLKPCVKLTPLCVTLNCKDVNATNTTNDSEGTMERGEIKNCSFNITTSIRDKVQKEYALFYKLDVVPIDNNNTSYRLISCNTSVITQACPKISFEPIPIHYCAPAGFAILKCNDKTFNGTGPCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKTIIVQLKESVEINCTRPNNNTRKSIHIGPGRAFYTTGEIIGDIRQAHCNISRAKWNDTLKQIVIKLREQFENKTIVFNHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNNNTEGSNNTEGNTITLPCRIKQIINMWQEVGGCGAMYAPPIRGQIRCSSNITGLLLTRDGGINENGTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GTLVRDN
CDRH2HDSGD
CDRH3TKHGRRIYGVVAFKEWFTYFYMDV
CDRL1GEESLGSRSVI
CDRL2NNNDRPS
CDRL3HIWDSRRPTNWV

Orientation Angles (from ABangle)
HL-63.2°
HC179.55°
HC2122.28°
LC1118.97°
LC289.98°
dc17.44Å
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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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