Structure Viewer: 7mxd

>   Structure details

Cryo-Em Structure of Broadly Neutralizing V2-apex-Targeting antibody J038 in complex with Hiv-1 Env

PDB7mxd
SpeciesHOMO SAPIENS; MACACA MULATTA
MethodELECTRON MICROSCOPY
Resolution3.4Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
>   Structure visualisation
Please note the WebGL plugin needs to be enabled to use PV Viewer.

Display options:














>   Fv information

This PDB has 4 Fv(s).

>   J/K
Fv Details
Heavy chainJ
Light chainK
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 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 76A 76B 76C 76D 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L L Q S G A A V T K P G A S V R V S C E A S G Y N I R D Y F I H W W R Q A P G Q G L Q W V G W I N P K T G Q P N N P R Q F Q G R V S L T R H A S W D F D T Y S F Y M D L K A L R S D D T A V Y F C A R Q R S D Y W D F D V W G S G T Q 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 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q M T Q S P S S L S A S V G D T V T I T C Q A N G Y L N W Y Q Q R R G K A P K L L I Y D G S K L E R G V P S R F S G R R W G Q E Y N L T I N N L Q P E D I A T Y F C Q V Y E F V V P G T R L D L K

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

CDR Sequences (chothia definition)
CDRH1GYNIRDY
CDRH2NPKTGQ
CDRH3QRSDYWDFDV
CDRL1QANGYLN
CDRL2DGSKLER
CDRL3QVYEF

Orientation Angles (from ABangle)
HL-56.87°
HC173.11°
HC2112.88°
LC1123.64°
LC284.99°
dc17.07Å
>   C/D
Fv Details
Heavy chainC
Light chainD
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 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 76A 76B 76C 76D 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L L Q S G A A V T K P G A S V R V S C E A S G Y N I R D Y F I H W W R Q A P G Q G L Q W V G W I N P K T G Q P N N P R Q F Q G R V S L T R H A S W D F D T Y S F Y M D L K A L R S D D T A V Y F C A R Q R S D Y W D F D V W G S G T Q 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 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q M T Q S P S S L S A S V G D T V T I T C Q A N G Y L N W Y Q Q R R G K A P K L L I Y D G S K L E R G V P S R F S G R R W G Q E Y N L T I N N L Q P E D I A T Y F C Q V Y E F V V P G T R L D L K

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

CDR Sequences (chothia definition)
CDRH1GYNIRDY
CDRH2NPKTGQ
CDRH3QRSDYWDFDV
CDRL1QANGYLN
CDRL2DGSKLER
CDRL3QVYEF

Orientation Angles (from ABangle)
HL-56.45°
HC174.15°
HC2113.69°
LC1123.86°
LC286.2°
dc17.0Å
>   X/Y
Fv Details
Heavy chainX
Light chainY
Heavy subgroupunknown
Light subgroupIGKV1
SpeciesMACACA MULATTA
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q L H L Q E S G P G L V R P S E T L S L T C D V S G G A F N D A Y C S W I R R F P G G G L E W I G R I S G R D G Y V E S N P A L T G R V T M S I D A T W K K I V L R L T S M T A S D T A T Y F C A G E T P E D D F G Y Y Q P Y F K T W G Q G L G 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
D I Q L I Q S P S S V S A S L G D R V T I T C R S T Q G I G S D L A W Y Q A T P G T A P K L L I Y N S F A L H K G V P S R F S G S G S G T E F S L T I T G L Q P E D F A T Y Y C Q H Y R R L P L T F G G G T N I E V K

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

CDR Sequences (chothia definition)
CDRH1GGAFNDA
CDRH2SGRDGY
CDRH3ETPEDDFGYYQPYFKT
CDRL1RSTQGIGSDLA
CDRL2NSFALHK
CDRL3QHYRRLPLT

Orientation Angles (from ABangle)
HL-57.25°
HC174.58°
HC2119.34°
LC1121.65°
LC284.55°
dc16.61Å
>   S/U
Fv Details
Heavy chainS
Light chainU
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 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 76A 76B 76C 76D 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L L Q S G A A V T K P G A S V R V S C E A S G Y N I R D Y F I H W W R Q A P G Q G L Q W V G W I N P K T G Q P N N P R Q F Q G R V S L T R H A S W D F D T Y S F Y M D L K A L R S D D T A V Y F C A R Q R S D Y W D F D V W G S G T Q 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 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 96 97 98 99 100 101 102 103 104 105 106 107
D I Q M T Q S P S S L S A S V G D T V T I T C Q A N G Y L N W Y Q Q R R G K A P K L L I Y D G S K L E R G V P S R F S G R R W G Q E Y N L T I N N L Q P E D I A T Y F C Q V Y E F V V P G T R L D L K

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

CDR Sequences (chothia definition)
CDRH1GYNIRDY
CDRH2NPKTGQ
CDRH3QRSDYWDFDV
CDRL1QANGYLN
CDRL2DGSKLER
CDRL3QVYEF

Orientation Angles (from ABangle)
HL-55.58°
HC173.44°
HC2113.4°
LC1124.63°
LC286.7°
dc17.01Å
>   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]

Our privacy policy