Structure Viewer: 2jix

>   Structure details

Crystal Structure of abt-007 Fab Fragment with the Soluble Domain of Epo Receptor

PDB2jix
SpeciesSYNTHETIC CONSTRUCT
MethodX-RAY DIFFRACTION
Resolution3.2Å
Number of Fvs3
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 3 Fv(s).

>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesSYNTHETIC CONSTRUCT
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 53 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C T V S G A S I S S Y Y W S W I R Q P P G K G L E W I G Y I G G E G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L R S V T A A D T A V Y Y C A R E R L G I G D 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 L T Q S P S S L S A S V G D R V T I T C R A S Q G I R N D L G W Y Q Q K P G K A P K R L I Y A A S S L Q 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 L Q H N T Y P P T F G Q G T K V E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen nameerythropoietin receptor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLD

CDR Sequences (chothia definition)
CDRH1GASISSY
CDRH2GGEGS
CDRH3ERLGIGDY
CDRL1RASQGIRNDLG
CDRL2AASSLQS
CDRL3LQHNTYPPT

Orientation Angles (from ABangle)
HL-60.02°
HC171.97°
HC2117.51°
LC1120.9°
LC285.08°
dc16.03Å
>   F/A
Fv Details
Heavy chainF
Light chainA
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesSYNTHETIC CONSTRUCT
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 53 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C T V S G A S I S S Y Y W S W I R Q P P G K G L E W I G Y I G G E G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L R S V T A A D T A V Y Y C A R E R L G I G D 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 L T Q S P S S L S A S V G D R V T I T C R A S Q G I R N D L G W Y Q Q K P G K A P K R L I Y A A S S L Q 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 L Q H N T Y P P T F G Q G T K V E I K

Antigen Details
Antigen chainsC,B
Antigen typeprotein
Antigen nameerythropoietin receptor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLD/APPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLD

CDR Sequences (chothia definition)
CDRH1GASISSY
CDRH2GGEGS
CDRH3ERLGIGDY
CDRL1RASQGIRNDLG
CDRL2AASSLQS
CDRL3LQHNTYPPT

Orientation Angles (from ABangle)
HL-62.22°
HC172.25°
HC2117.14°
LC1119.88°
LC283.83°
dc15.97Å
>   D/G
Fv Details
Heavy chainD
Light chainG
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesSYNTHETIC CONSTRUCT
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 53 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113
Q V Q L Q E S G P G L V K P S E T L S L T C T V S G A S I S S Y Y W S W I R Q P P G K G L E W I G Y I G G E G S T N Y N P S L K S R V T I S V D T S K N Q F S L K L R S V T A A D T A V Y Y C A R E R L G I G D 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 L T Q S P S S L S A S V G D R V T I T C R A S Q G I R N D L G W Y Q Q K P G K A P K R L I Y A A S S L Q 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 L Q H N T Y P P T F G Q G T K V E I K

Antigen Details
Antigen chainsE
Antigen typeprotein
Antigen nameerythropoietin receptor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPPPNLPDPKFESKAALLAARGPEELLCFTERLEDLVCFWEEAASAGVGPGNYSFSYQLEDEPWKLCRLHQAPTARGAVRFWCSLPTADTSSFVPLELRVTAASGAPRYHRVIHINEVVLLDAPVGLVARLADESGHVVLRWLPPPETPMTSHIRYEVDVSAGNGAGSVQRVEILEGRTECVLSNLRGRTRYTFAVRARMAEPSFGGFWSAWSEPVSLLTPSDLD

CDR Sequences (chothia definition)
CDRH1GASISSY
CDRH2GGEGS
CDRH3ERLGIGDY
CDRL1RASQGIRNDLG
CDRL2AASSLQS
CDRL3LQHNTYPPT

Orientation Angles (from ABangle)
HL-63.66°
HC170.46°
HC2116.69°
LC1119.6°
LC284.17°
dc16.13Å
>   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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