Structure Viewer: 8t49

>   Structure details

Md65 N332-Gt5 Sosip in complex with Rm_N332_03 Fab and Rm20a3 Fab

PDB8t49
SpeciesMACACA MULATTA
MethodELECTRON MICROSCOPY
Resolution3.2Å
Number of Fvs6
In complexTrue
Light chain typeLambda
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGLV3
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 31A 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 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 E T L S L T C I V S G D S I S S S E W W S W I R Q P P G K G L E W I G N I G G S S G S T Y Y N A S L K S R V T I S K D T S K N Q F S L E L K S V T A A D T A V Y Y C A R S S I T I F G V V V L G E V E D K P L D V W G R G V L 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 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107
S S G L T Q E P A L S V A L G H T V S M T C Q G D S L E T Y Y V N W F Q Q R P G Q V P V L V V Y G N N Y R P S G I P E R F S G S W S G N T G T L T I T A A Q V E D E A D Y Y C N S W D S S G T H L L F G G G T R L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen namemd65 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCQNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTSVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRTVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GDSISSSE
CDRH2GGSSGS
CDRH3SSITIFGVVVLGEVEDKPLDV
CDRL1QGDSLETYYVN
CDRL2GNNYRPS
CDRL3NSWDSSGTHLL

Orientation Angles (from ABangle)
HL-53.89°
HC172.24°
HC2121.71°
LC1123.3°
LC285.83°
dc16.54Å
>   C/D
Fv Details
Heavy chainC
Light chainD
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 chainsG
Antigen typeprotein
Antigen namemd65 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAAGIGASSDGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-62.32°
HC172.22°
HC2118.58°
LC1115.82°
LC282.95°
dc15.86Å
>   O/Q
Fv Details
Heavy chainO
Light chainQ
Heavy subgroupIGHV4
Light subgroupIGLV3
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 31A 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 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 E T L S L T C I V S G D S I S S S E W W S W I R Q P P G K G L E W I G N I G G S S G S T Y Y N A S L K S R V T I S K D T S K N Q F S L E L K S V T A A D T A V Y Y C A R S S I T I F G V V V L G E V E D K P L D V W G R G V L 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 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107
S S G L T Q E P A L S V A L G H T V S M T C Q G D S L E T Y Y V N W F Q Q R P G Q V P V L V V Y G N N Y R P S G I P E R F S G S W S G N T G T L T I T A A Q V E D E A D Y Y C N S W D S S G T H L L F G G G T R L T V L

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen namemd65 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCQNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTSVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRTVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GDSISSSE
CDRH2GGSSGS
CDRH3SSITIFGVVVLGEVEDKPLDV
CDRL1QGDSLETYYVN
CDRL2GNNYRPS
CDRL3NSWDSSGTHLL

Orientation Angles (from ABangle)
HL-53.89°
HC172.24°
HC2121.71°
LC1123.29°
LC285.83°
dc16.54Å
>   J/M
Fv Details
Heavy chainJ
Light chainM
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 chainsI
Antigen typeprotein
Antigen namemd65 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAAGIGASSDGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-62.32°
HC172.22°
HC2118.58°
LC1115.82°
LC282.95°
dc15.86Å
>   P/R
Fv Details
Heavy chainP
Light chainR
Heavy subgroupIGHV4
Light subgroupIGLV3
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 31A 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 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 E T L S L T C I V S G D S I S S S E W W S W I R Q P P G K G L E W I G N I G G S S G S T Y Y N A S L K S R V T I S K D T S K N Q F S L E L K S V T A A D T A V Y Y C A R S S I T I F G V V V L G E V E D K P L D V W G R G V L 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 95A 95B 96 97 98 99 100 101 102 103 104 105 106 107
S S G L T Q E P A L S V A L G H T V S M T C Q G D S L E T Y Y V N W F Q Q R P G Q V P V L V V Y G N N Y R P S G I P E R F S G S W S G N T G T L T I T A A Q V E D E A D Y Y C N S W D S S G T H L L F G G G T R L T V L

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen namemd65 n332-gt5 sosip gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPKLRSMMRGEIKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCQNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTSVQINCTRPSNNTVKSIRIGPGQAFYYFGDVLGHVRMAHCNISKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSLILPCWIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRTVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GDSISSSE
CDRH2GGSSGS
CDRH3SSITIFGVVVLGEVEDKPLDV
CDRL1QGDSLETYYVN
CDRL2GNNYRPS
CDRL3NSWDSSGTHLL

Orientation Angles (from ABangle)
HL-53.89°
HC172.24°
HC2121.71°
LC1123.29°
LC285.83°
dc16.54Å
>   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 namemd65 n332-gt5 sosip gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAAGIGASSDGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-62.32°
HC172.22°
HC2118.58°
LC1115.82°
LC282.95°
dc15.86Å
>   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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