Structure Viewer: 4r2g

>   Structure details

Crystal Structure of Pgt124 Fab Bound to Hiv-1 Jrcsf Gp120 Core and to Cd4

PDB4r2g
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.283Å
Number of Fvs4
In complexTrue
Light chain typeLambda
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   N/M
Fv Details
Heavy chainN
Light chainM
Heavy subgroupIGHV4
Light subgroupIGLV3
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 52B 53 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 Q L Q E S G P G L V R P S E T L S V T C I V S G G S I S N Y Y W T W I R Q S P G K G L E W I G Y I S D R E T T T Y N P S L N S R A V I S R D T S K N Q L S L Q L R S V T T A D T A I Y F C A T A R R G Q R I Y G V V S F G E F F Y Y Y Y M D V W G K G T A V T V S S

Light chain

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 66A 66B 66C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S P L S V A L G E T A R I S C G R Q A L G S R A V Q W Y Q H K P G Q A P I L L I Y N N Q D R P S G I P E R F S G T P D I N F G T T A T L T I S G V E V G D E A D Y Y C H M W D S R S G F S W S F G G A T R L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namesurface protein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (JRCSFISOLATE)
Antigen sequenceDFNMWKNNMVEQMQEDVINLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGKGQCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEKVVIRSDNFTDNAKTIIVQLNESVKINCTRPSNNTRPGEIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFNNKTIVFTHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEKSSGTEGNDTIILPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGKNESEIEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGSISNY
CDRH2SDRET
CDRH3ARRGQRIYGVVSFGEFFYYYYMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-52.53°
HC172.93°
HC2122.7°
LC1129.88°
LC291.43°
dc16.79Å
>   J/I
Fv Details
Heavy chainJ
Light chainI
Heavy subgroupIGHV4
Light subgroupIGLV3
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 52B 53 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 Q L Q E S G P G L V R P S E T L S V T C I V S G G S I S N Y Y W T W I R Q S P G K G L E W I G Y I S D R E T T T Y N P S L N S R A V I S R D T S K N Q L S L Q L R S V T T A D T A I Y F C A T A R R G Q R I Y G V V S F G E F F Y Y Y Y M D V W G K G T A V T V S S

Light chain

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 66A 66B 66C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S P L S V A L G E T A R I S C G R Q A L G S R A V Q W Y Q H K P G Q A P I L L I Y N N Q D R P S G I P E R F S G T P D I N F G T T A T L T I S G V E V G D E A D Y Y C H M W D S R S G F S W S F G G A T R L T V L

Antigen Details
Antigen chainsK
Antigen typeprotein
Antigen namesurface protein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (JRCSFISOLATE)
Antigen sequenceDFNMWKNNMVEQMQEDVINLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGKGQCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEKVVIRSDNFTDNAKTIIVQLNESVKINCTRPSNNTRPGEIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFNNKTIVFTHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEKSSGTEGNDTIILPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGKNESEIEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGSISNY
CDRH2SDRET
CDRH3ARRGQRIYGVVSFGEFFYYYYMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-52.51°
HC173.15°
HC2122.82°
LC1130.03°
LC291.73°
dc16.84Å
>   D/C
Fv Details
Heavy chainD
Light chainC
Heavy subgroupIGHV4
Light subgroupIGLV3
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 52B 53 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 Q L Q E S G P G L V R P S E T L S V T C I V S G G S I S N Y Y W T W I R Q S P G K G L E W I G Y I S D R E T T T Y N P S L N S R A V I S R D T S K N Q L S L Q L R S V T T A D T A I Y F C A T A R R G Q R I Y G V V S F G E F F Y Y Y Y M D V W G K G T A V T V S S

Light chain

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 66A 66B 66C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S P L S V A L G E T A R I S C G R Q A L G S R A V Q W Y Q H K P G Q A P I L L I Y N N Q D R P S G I P E R F S G T P D I N F G T T A T L T I S G V E V G D E A D Y Y C H M W D S R S G F S W S F G G A T R L T V L

Antigen Details
Antigen chainsO
Antigen typeprotein
Antigen namesurface protein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (JRCSFISOLATE)
Antigen sequenceDFNMWKNNMVEQMQEDVINLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGKGQCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEKVVIRSDNFTDNAKTIIVQLNESVKINCTRPSNNTRPGEIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFNNKTIVFTHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEKSSGTEGNDTIILPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGKNESEIEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGSISNY
CDRH2SDRET
CDRH3ARRGQRIYGVVSFGEFFYYYYMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-52.71°
HC172.66°
HC2122.69°
LC1129.77°
LC291.98°
dc16.89Å
>   Q/P
Fv Details
Heavy chainQ
Light chainP
Heavy subgroupIGHV4
Light subgroupIGLV3
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 52B 53 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 Q L Q E S G P G L V R P S E T L S V T C I V S G G S I S N Y Y W T W I R Q S P G K G L E W I G Y I S D R E T T T Y N P S L N S R A V I S R D T S K N Q L S L Q L R S V T T A D T A I Y F C A T A R R G Q R I Y G V V S F G E F F Y Y Y Y M D V W G K G T A V T V S S

Light chain

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 66A 66B 66C 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 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
S P L S V A L G E T A R I S C G R Q A L G S R A V Q W Y Q H K P G Q A P I L L I Y N N Q D R P S G I P E R F S G T P D I N F G T T A T L T I S G V E V G D E A D Y Y C H M W D S R S G F S W S F G G A T R L T V L

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namesurface protein gp160
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (JRCSFISOLATE)
Antigen sequenceDFNMWKNNMVEQMQEDVINLWDQSLKPCVKLTGGSVITQACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGKGQCKNVSTVQCTHGIRPVVSTQLLLNGSLAEEKVVIRSDNFTDNAKTIIVQLNESVKINCTRPSNNTRPGEIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFNNKTIVFTHSSGGDPEIVMHSFNCGGEFFYCNSTQLFNSTWNDTEKSSGTEGNDTIILPCRIKQIINMWQEVGKAMYAPPIKGQIRCSSNITGLLLTRDGGKNESEIEIFRPGGGDMRDNWRSELYKYKVVKIE

CDR Sequences (chothia definition)
CDRH1GGSISNY
CDRH2SDRET
CDRH3ARRGQRIYGVVSFGEFFYYYYMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-51.96°
HC173.04°
HC2122.4°
LC1130.07°
LC291.84°
dc16.86Å
>   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]

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