Structure Viewer: 7t9b

>   Structure details

apexgt5 in complex with Gt5-D42.16 and Rm20a3 Fabs

PDB7t9b
SpeciesMACACA MULATTA; MUS MUSCULUS
MethodELECTRON MICROSCOPY
Resolution3.72Å
Number of Fvs4
In complexTrue
Light chain typeLambda,Kappa
Has constant regionFalse
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>   Fv information

This PDB has 4 Fv(s).

>   J/K
Fv Details
Heavy chainJ
Light chainK
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 chainsF
Antigen typeprotein
Antigen namehiv-1 envelope apexgt5 gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-61.7°
HC172.58°
HC2118.26°
LC1115.4°
LC283.32°
dc15.89Å
>   M/N
Fv Details
Heavy chainM
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 envelope apexgt5 gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-62.14°
HC172.75°
HC2118.26°
LC1115.79°
LC283.64°
dc15.84Å
>   O/P
Fv Details
Heavy chainO
Light chainP
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 envelope apexgt5 gp41
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

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

Orientation Angles (from ABangle)
HL-62.17°
HC172.55°
HC2118.47°
LC1115.86°
LC283.19°
dc15.92Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV3
SpeciesMUS MUSCULUS
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 52B 52C 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 100N 100O 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G L V K P G G S L R L S C T A S G F T F S N A W M S W V R Q A P G K G L E W V G R I K S K T E G G T T D Y A T P V K G R F T I S R D D S K D T L F L Q M N S L K T E D T A V Y Y C N T G V E T Y D F W S G Y D D H Y Y D Y Y F R D V W G K G T T V T 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 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 96 97 98 99 100 101 102 103 104 105 106 107
E I V L T Q S P G T L S L S P G E R A T L S C R A S Q I I S S I Y F A W Y Q Q K P G Q A P R L L I Y G A S S R A T G I P D R F S G S G S G T D F T L T I S R L E P E D F A V Y Y C Q Q Y G S S F T F G P G T K V D I K

Antigen Details
Antigen chainsE,C,A
Antigen typeprotein
Antigen namehiv-1 envelope apexgt5 gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceAENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNATTELRNKRQKVYSLFYRLDIVPMVDLWTNYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNATTELRNKRQKVYSLFYRLDIVPMVDLWTNYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR/AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNATTELRNKRQKVYSLFYRLDIVPMVDLWTNYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

CDR Sequences (chothia definition)
CDRH1GFTFSNA
CDRH2KSKTEGGT
CDRH3GVETYDFWSGYDDHYYDYYFRDV
CDRL1RASQIISSIYFA
CDRL2GASSRAT
CDRL3QQYGSSFT

Orientation Angles (from ABangle)
HL-63.5°
HC170.62°
HC2121.08°
LC1120.14°
LC283.91°
dc16.28Å
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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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