Structure Viewer: 6xsw

>   Structure details

Structure of the Notch3 Nrr in complex with an antibody Fab Fragment

PDB6xsw
SpeciesRATTUS NORVEGICUS
MethodX-RAY DIFFRACTION
Resolution2.98Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesRATTUS NORVEGICUS
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 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 Q L V E S G G G L V Q P G G S L R L S C A A S G Y A F T D Y W M T W V R Q A P G K G L E W V A E I S P N S G G T N F N E K F K G R F T I S V D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R G E I R Y N W F A Y W G Q G T L 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 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 Q M T Q S P S S L S A S V G D R V T I T C K A S Q N V G N N I A W Y Q Q K P G K A P K L L I Y Y A S N R Y T G V P S R F S G S G Y G T D F T L T I S S L Q P E D F A T Y Y C Q R L Y N S P F T F G G G T K V E I K

Antigen Details
Antigen chainsC
Antigen typeprotein
Antigen nameneurogenic locus notch homolog protein 3
Antigen speciesHOMO SAPIENS
Antigen sequenceMETDTLLLWVLLLWVPGSTGGSGHHHHHHGENLYFQSAPEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNSRCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDAHGQAMVFPYHRPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPL

CDR Sequences (chothia definition)
CDRH1GYAFTDY
CDRH2SPNSGG
CDRH3GEIRYNWFAY
CDRL1KASQNVGNNIA
CDRL2YASNRYT
CDRL3QRLYNSPFT

Orientation Angles (from ABangle)
HL-55.44°
HC173.21°
HC2119.23°
LC1121.84°
LC281.87°
dc16.13Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesRATTUS NORVEGICUS
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 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 Q L V E S G G G L V Q P G G S L R L S C A A S G Y A F T D Y W M T W V R Q A P G K G L E W V A E I S P N S G G T N F N E K F K G R F T I S V D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R G E I R Y N W F A Y W G Q G T L 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 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 Q M T Q S P S S L S A S V G D R V T I T C K A S Q N V G N N I A W Y Q Q K P G K A P K L L I Y Y A S N R Y T G V P S R F S G S G Y G T D F T L T I S S L Q P E D F A T Y Y C Q R L Y N S P F T F G G G T K V E I K

Antigen Details
Antigen chainsX
Antigen typeprotein
Antigen nameneurogenic locus notch homolog protein 3
Antigen speciesHOMO SAPIENS
Antigen sequenceMETDTLLLWVLLLWVPGSTGGSGHHHHHHGENLYFQSAPEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNSRCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDAHGQAMVFPYHRPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPL

CDR Sequences (chothia definition)
CDRH1GYAFTDY
CDRH2SPNSGG
CDRH3GEIRYNWFAY
CDRL1KASQNVGNNIA
CDRL2YASNRYT
CDRL3QRLYNSPFT

Orientation Angles (from ABangle)
HL-55.65°
HC173.18°
HC2119.23°
LC1121.43°
LC281.71°
dc16.13Å
>   G/I
Fv Details
Heavy chainG
Light chainI
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesRATTUS NORVEGICUS
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 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 Q L V E S G G G L V Q P G G S L R L S C A A S G Y A F T D Y W M T W V R Q A P G K G L E W V A E I S P N S G G T N F N E K F K G R F T I S V D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R G E I R Y N W F A Y W G Q G T L 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 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 Q M T Q S P S S L S A S V G D R V T I T C K A S Q N V G N N I A W Y Q Q K P G K A P K L L I Y Y A S N R Y T G V P S R F S G S G Y G T D F T L T I S S L Q P E D F A T Y Y C Q R L Y N S P F T F G G G T K V E I K

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen nameneurogenic locus notch homolog protein 3
Antigen speciesHOMO SAPIENS
Antigen sequenceMETDTLLLWVLLLWVPGSTGGSGHHHHHHGENLYFQSAPEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNSRCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDAHGQAMVFPYHRPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPL

CDR Sequences (chothia definition)
CDRH1GYAFTDY
CDRH2SPNSGG
CDRH3GEIRYNWFAY
CDRL1KASQNVGNNIA
CDRL2YASNRYT
CDRL3QRLYNSPFT

Orientation Angles (from ABangle)
HL-54.79°
HC172.55°
HC2119.07°
LC1120.75°
LC282.7°
dc16.16Å
>   D/E
Fv Details
Heavy chainD
Light chainE
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesRATTUS NORVEGICUS
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 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 Q L V E S G G G L V Q P G G S L R L S C A A S G Y A F T D Y W M T W V R Q A P G K G L E W V A E I S P N S G G T N F N E K F K G R F T I S V D N A K N S L Y L Q M N S L R A E D T A V Y Y C A R G E I R Y N W F A Y W G Q G T L 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 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 Q M T Q S P S S L S A S V G D R V T I T C K A S Q N V G N N I A W Y Q Q K P G K A P K L L I Y Y A S N R Y T G V P S R F S G S G Y G T D F T L T I S S L Q P E D F A T Y Y C Q R L Y N S P F T F G G G T K V E I K

Antigen Details
Antigen chainsF
Antigen typeprotein
Antigen nameneurogenic locus notch homolog protein 3
Antigen speciesHOMO SAPIENS
Antigen sequenceMETDTLLLWVLLLWVPGSTGGSGHHHHHHGENLYFQSAPEVSEEPRCPRAACQAKRGDQRCDRECNSPGCGWDGGDCSLSVGDPWRQCEALQCWRLFNNSRCDPACSSPACLYDNFDCHAGGRERTCNPVYEKYCADHFADGRCDQGCNTEECGWDGLDCASEVPALLARGVLVLTVLLPPEELLRSSADFLQRLSAILRTSLRFRLDAHGQAMVFPYHRPEVIGSVVMLEIDNRLCLQSPENDHCFPDAQSAADYLGALSAVERLDFPYPLRDVRGEPL

CDR Sequences (chothia definition)
CDRH1GYAFTDY
CDRH2SPNSGG
CDRH3GEIRYNWFAY
CDRL1KASQNVGNNIA
CDRL2YASNRYT
CDRL3QRLYNSPFT

Orientation Angles (from ABangle)
HL-54.49°
HC172.9°
HC2120.05°
LC1120.59°
LC282.66°
dc16.3Å
>   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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