Structure Viewer: 7zlk

>   Structure details

amc009 Sosipv5.2 in complex with Fabs acs101 and acs124

PDB7zlk
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution
Number of Fvs5
In complexTrue
Light chain typeLambda,Kappa
Has constant regionFalse
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>   Fv information

This PDB has 5 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q W G G G L L K P S Q T L S L T C A V Y R W T F N D H Y W S W V R Q S P G K G L E W I G E I S W G G A T N Y N P S L K S R V T M S V D T S M S H V S L K M T S V T A A D T G V Y Y C V R V G P G P H M A A L D Y W G H G S R V L 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 30A 30B 30C 30D 30E 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 V M T Q T P L S S P V T L G Q P A S I S C G S S Q S L V H S D G N T Y L S W L Q Q R P G Q P P R L L I Y K I S N R I S G L P D R F S G S G A E T N F T L K I S R V E A E D V G L Y Y C V Q G T Q F P W T S G Q G T K V E I K

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen nameamc009 sosipv5.2 envelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1RWTFNDH
CDRH2SWGGA
CDRH3VGPGPHMAALDY
CDRL1GSSQSLVHSDGNTYLS
CDRL2KISNRIS
CDRL3VQGTQFPWT

Orientation Angles (from ABangle)
HL-60.19°
HC173.49°
HC2119.45°
LC1120.16°
LC281.09°
dc15.99Å
>   M/N
Fv Details
Heavy chainM
Light chainN
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 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 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 A L S L T C S V S G V A I S R H Y W N W I R Q P P G K G L E W I G Y I F F N G N T N Y S P S L K S R V T I S V D T S K N E F S L T L R S V T A A D T A V Y Y C A R E K S V V E P D N M V R W F D P W G Q G T 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 Y E L T Q P P S V S V A P G K T A R I T C G G N N I G S K S V H W Y Q Q K P G Q A P V L V I Y Y D S D R P S G I P E R F S G S K S G N T A T L T I S R V E A G D E A D Y Y C Q V W D S S R D H C V F G I G T K V T V L

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen nameamc009 sosipv5.2 envelope glycoprotein gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD

CDR Sequences (chothia definition)
CDRH1GVAISRH
CDRH2FFNGN
CDRH3EKSVVEPDNMVRWFDP
CDRL1GGNNIGSKSVH
CDRL2YDSDRPS
CDRL3QVWDSSRDHCV

Orientation Angles (from ABangle)
HL-55.61°
HC173.48°
HC2120.11°
LC1121.45°
LC285.44°
dc16.59Å
>   O/P
Fv Details
Heavy chainO
Light chainP
Heavy subgroupIGHV4
Light subgroupIGKV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q W G G G L L K P S Q T L S L T C A V Y R W T F N D H Y W S W V R Q S P G K G L E W I G E I S W G G A T N Y N P S L K S R V T M S V D T S M S H V S L K M T S V T A A D T G V Y Y C V R V G P G P H M A A L D Y W G H G S R V L 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 30A 30B 30C 30D 30E 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 V M T Q T P L S S P V T L G Q P A S I S C G S S Q S L V H S D G N T Y L S W L Q Q R P G Q P P R L L I Y K I S N R I S G L P D R F S G S G A E T N F T L K I S R V E A E D V G L Y Y C V Q G T Q F P W T S G Q G T K V E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameamc009 sosipv5.2 envelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1RWTFNDH
CDRH2SWGGA
CDRH3VGPGPHMAALDY
CDRL1GSSQSLVHSDGNTYLS
CDRL2KISNRIS
CDRL3VQGTQFPWT

Orientation Angles (from ABangle)
HL-61.09°
HC176.18°
HC2119.79°
LC1118.82°
LC281.08°
dc15.59Å
>   Q/R
Fv Details
Heavy chainQ
Light chainR
Heavy subgroupIGHV4
Light subgroupIGKV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q Q W G G G L L K P S Q T L S L T C A V Y R W T F N D H Y W S W V R Q S P G K G L E W I G E I S W G G A T N Y N P S L K S R V T M S V D T S M S H V S L K M T S V T A A D T G V Y Y C V R V G P G P H M A A L D Y W G H G S R V L 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 30A 30B 30C 30D 30E 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 V M T Q T P L S S P V T L G Q P A S I S C G S S Q S L V H S D G N T Y L S W L Q Q R P G Q P P R L L I Y K I S N R I S G L P D R F S G S G A E T N F T L K I S R V E A E D V G L Y Y C V Q G T Q F P W T S G Q G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameamc009 sosipv5.2 envelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceARADKLWVTVYYGVPVWKEATTTLFCASDAKAYDTEVRNVWATHCCVPTDPNPQEVVLENVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCTDYVGNATNASTTNATGGIGGTVERGEIKNCSFNITTSIRDKVQKEYALFYKLDIVPIDNDNTNNSYRLINCNTSVIKQACPKVSFEPIPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEKEVVIRSQNFTNNAKVIIVQLNESVVINCTRPNNNTRKSIHIAPGRWFYTTGAIIGDIRQAHCNISRVKWNNTLKQIATKLREQFKNKTIAFNQSSGGDPEIVMHSFNCGGEFFYCNTTQLFNSTWNDTEVSNYNDITHITLPCRIKQIINMWQKVGKAMYAPPIRGQIRCSSNITGLLLTRDGGSNENKTSETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKCKRRVVQ

CDR Sequences (chothia definition)
CDRH1RWTFNDH
CDRH2SWGGA
CDRH3VGPGPHMAALDY
CDRL1GSSQSLVHSDGNTYLS
CDRL2KISNRIS
CDRL3VQGTQFPWT

Orientation Angles (from ABangle)
HL-61.68°
HC173.99°
HC2118.78°
LC1120.27°
LC281.2°
dc16.01Å
>   S/T
Fv Details
Heavy chainS
Light chainT
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 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 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 A L S L T C S V S G V A I S R H Y W N W I R Q P P G K G L E W I G Y I F F N G N T N Y S P S L K S R V T I S V D T S K N E F S L T L R S V T A A D T A V Y Y C A R E K S V V E P D N M V R W F D P W G Q G T 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 Y E L T Q P P S V S V A P G K T A R I T C G G N N I G S K S V H W Y Q Q K P G Q A P V L V I Y Y D S D R P S G I P E R F S G S K S G N T A T L T I S R V E A G D E A D Y Y C Q V W D S S R D H C V F G I G T K V T V L

Antigen Details
Antigen chainsE,B
Antigen typeprotein
Antigen nameamc009 sosipv5.2 envelope glycoprotein gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD/AVGAIGAVFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQNNLLRAPECQQHMLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTAVPWNNSWSNRSLDMIWNNMTWIEWEREIDNYTGLIYNLLEESQNQQEKNEQELLELD

CDR Sequences (chothia definition)
CDRH1GVAISRH
CDRH2FFNGN
CDRH3EKSVVEPDNMVRWFDP
CDRL1GGNNIGSKSVH
CDRL2YDSDRPS
CDRL3QVWDSSRDHCV

Orientation Angles (from ABangle)
HL-54.25°
HC173.09°
HC2118.91°
LC1121.21°
LC284.93°
dc16.54Å
>   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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