Structure Viewer: 6nf5

>   Structure details

Bg505 Md64 N332-Gt5 Sosip Trimer in complex with Bg18-Like Precursor Hmp1 Fragmentantigen Binding and Base-Binding Rm20a3 Fragment antigen Binding

PDB6nf5
SpeciesMACACA MULATTA; HOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution3.71Å
Number of Fvs6
In complexTrue
Light chain typeLambda
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   G/I
Fv Details
Heavy chainG
Light chainI
Heavy subgroupIGHV3
Light subgroupIGLV2
SpeciesMACACA MULATTA
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 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
E V Q L V E T G G G L V Q P G G S L K L S C R A S G Y T F S S F A M S W V R Q A P G K G L E W V S L I N D R G G L T F Y V D S V K G R F T I S R D N S K N T L S L Q M H S L R D G D T A V Y Y C A T G G M S S A L Q S S K Y Y F D F W G Q G A L V T V S S

Light chain

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

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGTKHHHHHH

CDR Sequences (chothia definition)
CDRH1GYTFSSF
CDRH2NDRGGL
CDRH3GGMSSALQSSKYYFDF
CDRL1TGTSSDIGSYNYVS
CDRL2DVTQRPS
CDRL3SAYAGRQTFYI

Orientation Angles (from ABangle)
HL-62.53°
HC173.13°
HC2118.37°
LC1115.81°
LC283.18°
dc15.75Å
>   Q/R
Fv Details
Heavy chainQ
Light chainR
Heavy subgroupIGHV3
Light subgroupIGLV2
SpeciesMACACA MULATTA
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 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
E V Q L V E T G G G L V Q P G G S L K L S C R A S G Y T F S S F A M S W V R Q A P G K G L E W V S L I N D R G G L T F Y V D S V K G R F T I S R D N S K N T L S L Q M H S L R D G D T A V Y Y C A T G G M S S A L Q S S K Y Y F D F W G Q G A L V T V S S

Light chain

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

Antigen Details
Antigen chainsM
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGTKHHHHHH

CDR Sequences (chothia definition)
CDRH1GYTFSSF
CDRH2NDRGGL
CDRH3GGMSSALQSSKYYFDF
CDRL1TGTSSDIGSYNYVS
CDRL2DVTQRPS
CDRL3SAYAGRQTFYI

Orientation Angles (from ABangle)
HL-62.54°
HC173.13°
HC2118.37°
LC1115.81°
LC283.18°
dc15.75Å
>   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 31A 31B 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 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 K P S Q T L S L T C T V S G G S I S S G S Y Y W S W I R Q P A G K G L E W I G R I Y T S G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L S S V T A A D T A V Y Y C A R E G F T I F G V V T F S E G Y Y Y G M D V W G K G T T 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 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
S Y E L T Q P P S V S V S P G Q T A R I T C S G D A L P K Q Y A Y W Y Q Q K P G Q A P V L V I Y K D S E R P S G I P E R F S G S S S G T T V T L T I S G V Q A E D E A D Y Y C Q S A D S S G E V F G G G T K L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GGSISSGSY
CDRH2YTSGS
CDRH3EGFTIFGVVTFSEGYYYGMDV
CDRL1SGDALPKQYAY
CDRL2KDSERPS
CDRL3QSADSSGEV

Orientation Angles (from ABangle)
HL-58.36°
HC172.02°
HC2122.09°
LC1122.42°
LC280.76°
dc16.26Å
>   O/P
Fv Details
Heavy chainO
Light chainP
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 31A 31B 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 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 K P S Q T L S L T C T V S G G S I S S G S Y Y W S W I R Q P A G K G L E W I G R I Y T S G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L S S V T A A D T A V Y Y C A R E G F T I F G V V T F S E G Y Y Y G M D V W G K G T T 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 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
S Y E L T Q P P S V S V S P G Q T A R I T C S G D A L P K Q Y A Y W Y Q Q K P G Q A P V L V I Y K D S E R P S G I P E R F S G S S S G T T V T L T I S G V Q A E D E A D Y Y C Q S A D S S G E V F G G G T K L T V L

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GGSISSGSY
CDRH2YTSGS
CDRH3EGFTIFGVVTFSEGYYYGMDV
CDRL1SGDALPKQYAY
CDRL2KDSERPS
CDRL3QSADSSGEV

Orientation Angles (from ABangle)
HL-58.36°
HC172.02°
HC2122.08°
LC1122.42°
LC280.76°
dc16.26Å
>   K/N
Fv Details
Heavy chainK
Light chainN
Heavy subgroupIGHV3
Light subgroupIGLV2
SpeciesMACACA MULATTA
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 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
E V Q L V E T G G G L V Q P G G S L K L S C R A S G Y T F S S F A M S W V R Q A P G K G L E W V S L I N D R G G L T F Y V D S V K G R F T I S R D N S K N T L S L Q M H S L R D G D T A V Y Y C A T G G M S S A L Q S S K Y Y F D F W G Q G A L V T V S S

Light chain

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

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALDGTKHHHHHH

CDR Sequences (chothia definition)
CDRH1GYTFSSF
CDRH2NDRGGL
CDRH3GGMSSALQSSKYYFDF
CDRL1TGTSSDIGSYNYVS
CDRL2DVTQRPS
CDRL3SAYAGRQTFYI

Orientation Angles (from ABangle)
HL-62.54°
HC173.13°
HC2118.37°
LC1115.81°
LC283.18°
dc15.75Å
>   E/F
Fv Details
Heavy chainE
Light chainF
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 31A 31B 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 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 K P S Q T L S L T C T V S G G S I S S G S Y Y W S W I R Q P A G K G L E W I G R I Y T S G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L S S V T A A D T A V Y Y C A R E G F T I F G V V T F S E G Y Y Y G M D V W G K G T T 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 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
S Y E L T Q P P S V S V S P G Q T A R I T C S G D A L P K Q Y A Y W Y Q Q K P G Q A P V L V I Y K D S E R P S G I P E R F S G S S S G T T V T L T I S G V Q A E D E A D Y Y C Q S A D S S G E V F G G G T K L T V L

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen namehiv-1 env bg505 md64 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GGSISSGSY
CDRH2YTSGS
CDRH3EGFTIFGVVTFSEGYYYGMDV
CDRL1SGDALPKQYAY
CDRL2KDSERPS
CDRL3QSADSSGEV

Orientation Angles (from ABangle)
HL-58.36°
HC172.02°
HC2122.08°
LC1122.42°
LC280.76°
dc16.26Å
>   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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