Structure Viewer: 3ixx

>   Structure details

the Pseudo-atomic Structure of West Nile Immature Virus in complex with Fab Fragments of the anti-Fusion Loop antibody E53

PDB3ixx
SpeciesMUS MUSCULUS
MethodELECTRON MICROSCOPY
Resolution15Å
Number of Fvs2
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 2 Fv(s).

>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV7
Light subgroupIGKV4
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V K L V E S G G G L V L P G G S L R L S C A T S G F T F T D Y Y M T W V R Q P P G K A L E W L G F I G N K A N D Y T T E Y S A S V K G R F T I S R D D S Q S I L Y L Q M S T L R A E D R A T Y Y C A T V Y G N Y P Y F D V W G A G T T V A 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 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
Q I V L T Q S P A I M S A S P G E K V T M T C S A S S S V S Y M H W Y Q Q K S G T S P K I W I Y E S S K L A S G V P V R F S G S G S G T S Y S L T I S S M E A E D V A T Y Y C Q Q W S S H P H P L T F G A G T K L E L K

Antigen Details
Antigen chainsA
Antigen typeprotein
Antigen nameenvelope protein e
Antigen speciesWEST NILE VIRUS
Antigen sequenceFNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDVKMMNMEAANLAEVRSYCYLATVSDLSTKAACPTMGEAHNDKRADPAFVCRQGVVDRGWGNGCGLFGKGSIDTCAKFACSTKAIGRTILKENIKYEVAIFVHGPTTVESHGNYSTQVGATQAGRFSITPAAPSYTLKLGEYGEVTVDCEPRSGIDTNAYYVMTVGTKTFLVHREWFMDLNLPWSSAGSTVWRNRETLMEFEEPHATKQSVIALGSQEGALHQALAGAIPVEFSSNTVKLTSGHLKCRVKMEKLQLKGTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKS

CDR Sequences (chothia definition)
CDRH1GFTFTDY
CDRH2GNKANDYT
CDRH3VYGNYPYFDV
CDRL1SASSSVSYMH
CDRL2ESSKLAS
CDRL3QQWSSHPHPLT

Orientation Angles (from ABangle)
HL-64.94°
HC172.83°
HC2118.5°
LC1117.67°
LC281.61°
dc16.41Å
>   I/J
Fv Details
Heavy chainI
Light chainJ
Heavy subgroupIGHV7
Light subgroupIGKV4
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

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 101 102 103 104 105 106 107 108 109 110 111 112 113
E V K L V E S G G G L V L P G G S L R L S C A T S G F T F T D Y Y M T W V R Q P P G K A L E W L G F I G N K A N D Y T T E Y S A S V K G R F T I S R D D S Q S I L Y L Q M S T L R A E D R A T Y Y C A T V Y G N Y P Y F D V W G A G T T V A 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 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
Q I V L T Q S P A I M S A S P G E K V T M T C S A S S S V S Y M H W Y Q Q K S G T S P K I W I Y E S S K L A S G V P V R F S G S G S G T S Y S L T I S S M E A E D V A T Y Y C Q Q W S S H P H P L T F G A G T K L E L K

Antigen Details
Antigen chainsE,B
Antigen typeprotein
Antigen namepeptide pr; envelope protein e
Antigen speciesWEST NILE VIRUS
Antigen sequenceLSNFQGKVMMTVNATDVTDVITIPTAAGKNLCIVRAMDVGYMCDDTITYECPVLSAGNDPEDIDCWCTKSAVYVRYGRCT/FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDVKMMNMEAANLAEVRSYCYLATVSDLSTKAACPTMGEAHNDKRADPAFVCRQGVVDRGWGNGCGLFGKGSIDTCAKFACSTKAIGRTILKENIKYEVAIFVHGPTTVESHGNYSTQVGATQAGRFSITPAAPSYTLKLGEYGEVTVDCEPRSGIDTNAYYVMTVGTKTFLVHREWFMDLNLPWSSAGSTVWRNRETLMEFEEPHATKQSVIALGSQEGALHQALAGAIPVEFSSNTVKLTSGHLKCRVKMEKLQLKGTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKS

CDR Sequences (chothia definition)
CDRH1GFTFTDY
CDRH2GNKANDYT
CDRH3VYGNYPYFDV
CDRL1SASSSVSYMH
CDRL2ESSKLAS
CDRL3QQWSSHPHPLT

Orientation Angles (from ABangle)
HL-64.94°
HC172.83°
HC2118.5°
LC1117.67°
LC281.61°
dc16.41Å
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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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