Structure Viewer: 3ngb

>   Structure details

Crystal Structure of Broadly and Potently Neutralizing antibody Vrc01 in complex with Hiv-1 Gp120

PDB3ngb
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.68Å
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).

>   B/C
Fv Details
Heavy chainB
Light chainC
Heavy subgroupIGHV1
Light subgroupIGKV3
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G G Q M K K P G E S M R I S C R A S G Y E F I D C T L N W I R L A P G K R P E W M G W L K P R G G A V N Y A R P L Q G R V T M T R D V Y S D T A F L E L R S L T V D D T A V Y F C T R G K N C D Y N W D F E H W G R G T P V I 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 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 97 98 99 100 101 102 103 104 105 106
E I V L T Q S P G T L S L S P G E T A I I S C R T S Q Y G S L A W Y Q Q R P G Q A P R L V I Y S G S T R A A G I P D R F S G S R W G P D Y N L T I S N L E S G D F G V Y Y C Q Q Y E F F G Q G T K V Q V

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

CDR Sequences (chothia definition)
CDRH1GYEFIDC
CDRH2KPRGGA
CDRH3GKNCDYNWDFEH
CDRL1RTSQYGSLA
CDRL2SGSTRAA
CDRL3QQYEF

Orientation Angles (from ABangle)
HL-58.5°
HC176.44°
HC2113.76°
LC1126.54°
LC282.46°
dc15.41Å
>   J/K
Fv Details
Heavy chainJ
Light chainK
Heavy subgroupIGHV1
Light subgroupIGKV3
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G G Q M K K P G E S M R I S C R A S G Y E F I D C T L N W I R L A P G K R P E W M G W L K P R G G A V N Y A R P L Q G R V T M T R D V Y S D T A F L E L R S L T V D D T A V Y F C T R G K N C D Y N W D F E H W G R G T P V I 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 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 97 98 99 100 101 102 103 104 105 106
E I V L T Q S P G T L S L S P G E T A I I S C R T S Q Y G S L A W Y Q Q R P G Q A P R L V I Y S G S T R A A G I P D R F S G S R W G P D Y N L T I S N L E S G D F G V Y Y C Q Q Y E F F G Q G T K V Q V

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

CDR Sequences (chothia definition)
CDRH1GYEFIDC
CDRH2KPRGGA
CDRH3GKNCDYNWDFEH
CDRL1RTSQYGSLA
CDRL2SGSTRAA
CDRL3QQYEF

Orientation Angles (from ABangle)
HL-58.29°
HC176.57°
HC2113.58°
LC1126.52°
LC282.12°
dc15.32Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV1
Light subgroupIGKV3
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G G Q M K K P G E S M R I S C R A S G Y E F I D C T L N W I R L A P G K R P E W M G W L K P R G G A V N Y A R P L Q G R V T M T R D V Y S D T A F L E L R S L T V D D T A V Y F C T R G K N C D Y N W D F E H W G R G T P V I 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 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 97 98 99 100 101 102 103 104 105 106
E I V L T Q S P G T L S L S P G E T A I I S C R T S Q Y G S L A W Y Q Q R P G Q A P R L V I Y S G S T R A A G I P D R F S G S R W G P D Y N L T I S N L E S G D F G V Y Y C Q Q Y E F F G Q G T K V Q V

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen nameenvelope glycoprotein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceVWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITMHHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPIDGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

CDR Sequences (chothia definition)
CDRH1GYEFIDC
CDRH2KPRGGA
CDRH3GKNCDYNWDFEH
CDRL1RTSQYGSLA
CDRL2SGSTRAA
CDRL3QQYEF

Orientation Angles (from ABangle)
HL-58.24°
HC177.14°
HC2114.46°
LC1126.24°
LC282.48°
dc15.32Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGKV3
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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G G Q M K K P G E S M R I S C R A S G Y E F I D C T L N W I R L A P G K R P E W M G W L K P R G G A V N Y A R P L Q G R V T M T R D V Y S D T A F L E L R S L T V D D T A V Y F C T R G K N C D Y N W D F E H W G R G T P V I 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 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 97 98 99 100 101 102 103 104 105 106
E I V L T Q S P G T L S L S P G E T A I I S C R T S Q Y G S L A W Y Q Q R P G Q A P R L V I Y S G S T R A A G I P D R F S G S R W G P D Y N L T I S N L E S G D F G V Y Y C Q Q Y E F F G Q G T K V Q V

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

CDR Sequences (chothia definition)
CDRH1GYEFIDC
CDRH2KPRGGA
CDRH3GKNCDYNWDFEH
CDRL1RTSQYGSLA
CDRL2SGSTRAA
CDRL3QQYEF

Orientation Angles (from ABangle)
HL-57.75°
HC176.94°
HC2114.94°
LC1126.75°
LC282.06°
dc15.36Å
>   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