Structure Viewer: 7ugo

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Cryo-Em Structure of Bg24 inferred Germline Fabs with Mature Cdr3S and 10-1074 Fabs in complex with Hiv-1 Env Immunogen Bg505-Sosipv4.1-Gt1

PDB7ugo
SpeciesHOMO SAPIENS
MethodELECTRON MICROSCOPY
Resolution4.1Å
Number of Fvs6
In complexTrue
Light chain typeLambda,unknown
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   M/P
Fv Details
Heavy chainM
Light chainP
Heavy subgroupunknown
Light subgroupunknown
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 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 K P S E T L S V T C S V S G D S M N 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 S A T Y N P S L N S R V V I S R D T S K N Q L S L K L N S V T P A D T A V Y Y C A T A R R G Q R I Y G V V S F G E F F Y Y Y S M D V W G K G T T V T V S S

Light chain

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 68A 68B 68C 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
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 R 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 R A T L T I S G V E A 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 nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GDSMNNY
CDRH2SDRES
CDRH3ARRGQRIYGVVSFGEFFYYYSMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-53.6°
HC173.86°
HC2121.96°
LC1127.4°
LC289.73°
dc18.2Å
>   N/Q
Fv Details
Heavy chainN
Light chainQ
Heavy subgroupunknown
Light subgroupunknown
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 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 K P S E T L S V T C S V S G D S M N 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 S A T Y N P S L N S R V V I S R D T S K N Q L S L K L N S V T P A D T A V Y Y C A T A R R G Q R I Y G V V S F G E F F Y Y Y S M D V W G K G T T V T V S S

Light chain

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 68A 68B 68C 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
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 R 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 R A T L T I S G V E A 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 chainsB
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GDSMNNY
CDRH2SDRES
CDRH3ARRGQRIYGVVSFGEFFYYYSMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-53.77°
HC173.64°
HC2121.69°
LC1127.47°
LC289.69°
dc18.17Å
>   O/R
Fv Details
Heavy chainO
Light chainR
Heavy subgroupunknown
Light subgroupunknown
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 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 K P S E T L S V T C S V S G D S M N 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 S A T Y N P S L N S R V V I S R D T S K N Q L S L K L N S V T P A D T A V Y Y C A T A R R G Q R I Y G V V S F G E F F Y Y Y S M D V W G K G T T V T V S S

Light chain

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 68A 68B 68C 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
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 R 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 R A T L T I S G V E A 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 chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GDSMNNY
CDRH2SDRES
CDRH3ARRGQRIYGVVSFGEFFYYYSMDV
CDRL1GRQALGSRAVQ
CDRL2NNQDRPS
CDRL3HMWDSRSGFSWS

Orientation Angles (from ABangle)
HL-53.73°
HC173.8°
HC2121.95°
LC1127.42°
LC289.64°
dc18.17Å
>   G/J
Fv Details
Heavy chainG
Light chainJ
Heavy subgroupIGHV1
Light subgroupIGLV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y T F T G Y Y M H W V R Q A P G Q G L E W M G W I N P N S G G T N Y A Q K F Q G R V T M T R D T S I S T A Y M E L S R L R S D D T A V Y Y C A T Q V K L D S S A G Y P F D I W G Q G T M 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 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 96 97 98 99 100 101 102 103 104 105 106 107
Q S A L T Q P R S V S G S P G Q S V T I S C T G T S S D V G G Y N Y V S W Y Q Q H P G K A P K L M I Y D V S K R P S G V P D R F S G S K S G N T A S L T I S G L Q A E D E A D Y Y C S A F E Y F G G G T K L T V L

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GYTFTGY
CDRH2NPNSGG
CDRH3QVKLDSSAGYPFDI
CDRL1TGTSSDVGGYNYVS
CDRL2DVSKRPS
CDRL3SAFEY

Orientation Angles (from ABangle)
HL-55.85°
HC178.7°
HC2113.75°
LC1121.87°
LC286.63°
dc16.86Å
>   H/K
Fv Details
Heavy chainH
Light chainK
Heavy subgroupIGHV1
Light subgroupIGLV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y T F T G Y Y M H W V R Q A P G Q G L E W M G W I N P N S G G T N Y A Q K F Q G R V T M T R D T S I S T A Y M E L S R L R S D D T A V Y Y C A T Q V K L D S S A G Y P F D I W G Q G T M 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 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 96 97 98 99 100 101 102 103 104 105 106 107
Q S A L T Q P R S V S G S P G Q S V T I S C T G T S S D V G G Y N Y V S W Y Q Q H P G K A P K L M I Y D V S K R P S G V P D R F S G S K S G N T A S L T I S G L Q A E D E A D Y Y C S A F E Y F G G G T K L T V L

Antigen Details
Antigen chainsB
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GYTFTGY
CDRH2NPNSGG
CDRH3QVKLDSSAGYPFDI
CDRL1TGTSSDVGGYNYVS
CDRL2DVSKRPS
CDRL3SAFEY

Orientation Angles (from ABangle)
HL-55.76°
HC178.87°
HC2113.59°
LC1121.51°
LC286.98°
dc16.83Å
>   I/L
Fv Details
Heavy chainI
Light chainL
Heavy subgroupIGHV1
Light subgroupIGLV2
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 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L V Q S G A E V K K P G A S V K V S C K A S G Y T F T G Y Y M H W V R Q A P G Q G L E W M G W I N P N S G G T N Y A Q K F Q G R V T M T R D T S I S T A Y M E L S R L R S D D T A V Y Y C A T Q V K L D S S A G Y P F D I W G Q G T M 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 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 96 97 98 99 100 101 102 103 104 105 106 107
Q S A L T Q P R S V S G S P G Q S V T I S C T G T S S D V G G Y N Y V S W Y Q Q H P G K A P K L M I Y D V S K R P S G V P D R F S G S K S G N T A S L T I S G L Q A E D E A D Y Y C S A F E Y F G G G T K L T V L

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameenvelope glycoprotein gp120
Antigen speciesHUMAN IMMUNODEFICIENCY VIRUS 1
Antigen sequenceENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHACVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKRQKVHALFYKLDIVPINENQNTSYRLINCNTAAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMIRSEDIRNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQWFYATGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCDTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTDSTTETFRPSGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVV

CDR Sequences (chothia definition)
CDRH1GYTFTGY
CDRH2NPNSGG
CDRH3QVKLDSSAGYPFDI
CDRL1TGTSSDVGGYNYVS
CDRL2DVSKRPS
CDRL3SAFEY

Orientation Angles (from ABangle)
HL-55.9°
HC179.22°
HC2113.84°
LC1121.79°
LC286.92°
dc16.88Å
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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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