Structure Viewer: 6iw2

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Crystal Structure of 5a Scfv in complex with Yfv-17D Se in Prefusion State

PDB6iw2
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.9Å
Number of Fvs6
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 6 Fv(s).

>   K/L
Fv Details
Heavy chainK
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-56.81°
HC171.8°
HC2119.73°
LC1120.38°
LC283.12°
dc16.33Å
>   Q/R
Fv Details
Heavy chainQ
Light chainR
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsP
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-58.39°
HC171.12°
HC2119.32°
LC1120.74°
LC282.65°
dc16.39Å
>   N/O
Fv Details
Heavy chainN
Light chainO
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsM
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-57.97°
HC171.1°
HC2119.12°
LC1120.77°
LC282.92°
dc16.33Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsD
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-56.99°
HC172.15°
HC2119.58°
LC1120.55°
LC283.47°
dc16.31Å
>   B/C
Fv Details
Heavy chainB
Light chainC
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-58.26°
HC171.45°
HC2119.28°
LC1120.48°
LC283.11°
dc16.29Å
>   H/I
Fv Details
Heavy chainH
Light chainI
Heavy subgroupIGHV4
Light subgroupIGKV1
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 101 102 103 104 105 106 107 108 109 110
E V Q L V E S G P R L V K P S E T L S L T C T V S G G S T Y N H H W S W I R Q P P G R G L E W I G Y I S Y S G K S N Y N P S L K S R V T I S L E P S T T Q F S L K L N S L T A A D T A V Y Y C A R E Y R D D T N Y Y Y Y S L D V W G P G T M V T

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 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
Q I V M T Q S P S T L S A S V G D R V T I T C R A S Q S I G S W L A W Y Q Q K P G K A P K L L I Y K A S S L E S G V P S R F S G S G S G T E F T L T I S S L Q P E D F A T Y Y C Q Q Y N N Y S Y T F G P G T K L E I K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesYELLOW FEVER VIRUS (STRAIN 17D VACCINE)
Antigen sequenceAHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

CDR Sequences (chothia definition)
CDRH1GGSTYNH
CDRH2SYSGK
CDRH3EYRDDTNYYYYSLDV
CDRL1RASQSIGSWLA
CDRL2KASSLES
CDRL3QQYNNYSYT

Orientation Angles (from ABangle)
HL-57.21°
HC171.11°
HC2120.27°
LC1121.44°
LC283.19°
dc16.35Å
>   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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