Structure Viewer: 6bfq

>   Structure details

the Mechanism of Gm-Csf inhibition By Human Gm-Csf auto-antibodies

PDB6bfq
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.6Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

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

Antigen Details
Antigen chainsK
Antigen typeprotein
Antigen namegranulocyte-macrophage colony-stimulating factor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEPVQE

CDR Sequences (chothia definition)
CDRH1DSAIRKY
CDRH2YASGS
CDRH3ITGTTDL
CDRL1RASQGINRRLA
CDRL2AVSTLQS
CDRL3LQSNNYPLT

Orientation Angles (from ABangle)
HL-61.29°
HC172.87°
HC2118.9°
LC1122.61°
LC282.01°
dc16.37Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 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 99 101 102 103 104 105 106 107 108 109 110 111 112 113
M A Q L Q E S G P G V V K P S E T L S L T C S V S D S A I R K Y Y W S W I R Q P P G Q G L E Y I G Y I Y A S G S S F Y N P S F K S R V S M S V D A T N N Q F Y L K L T S V T A A D T A V Y Y C A A I T G T T D L W G R 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 V S A S V G D R V T I T C R A S Q G I N R R L A W Y Q Q K P G K A P K R L I Y A V S T L Q S G V P S R F N G S G S G T D F T L T V N N V Q P D D L A M Y F C L Q S N N Y P L T F G G G T K V E I K

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen namegranulocyte-macrophage colony-stimulating factor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEPVQE

CDR Sequences (chothia definition)
CDRH1DSAIRKY
CDRH2YASGS
CDRH3ITGTTDL
CDRL1RASQGINRRLA
CDRL2AVSTLQS
CDRL3LQSNNYPLT

Orientation Angles (from ABangle)
HL-61.39°
HC172.91°
HC2118.91°
LC1122.69°
LC281.71°
dc16.31Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 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 99 101 102 103 104 105 106 107 108 109 110 111 112 113
M A Q L Q E S G P G V V K P S E T L S L T C S V S D S A I R K Y Y W S W I R Q P P G Q G L E Y I G Y I Y A S G S S F Y N P S F K S R V S M S V D A T N N Q F Y L K L T S V T A A D T A V Y Y C A A I T G T T D L W G R 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 V S A S V G D R V T I T C R A S Q G I N R R L A W Y Q Q K P G K A P K R L I Y A V S T L Q S G V P S R F N G S G S G T D F T L T V N N V Q P D D L A M Y F C L Q S N N Y P L T F G G G T K V E I K

Antigen Details
Antigen chainsG
Antigen typeprotein
Antigen namegranulocyte-macrophage colony-stimulating factor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEPVQE

CDR Sequences (chothia definition)
CDRH1DSAIRKY
CDRH2YASGS
CDRH3ITGTTDL
CDRL1RASQGINRRLA
CDRL2AVSTLQS
CDRL3LQSNNYPLT

Orientation Angles (from ABangle)
HL-61.36°
HC173.18°
HC2119.06°
LC1121.99°
LC280.65°
dc16.38Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV4
Light subgroupIGKV1
SpeciesHOMO SAPIENS
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 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 99 101 102 103 104 105 106 107 108 109 110 111 112 113
M A Q L Q E S G P G V V K P S E T L S L T C S V S D S A I R K Y Y W S W I R Q P P G Q G L E Y I G Y I Y A S G S S F Y N P S F K S R V S M S V D A T N N Q F Y L K L T S V T A A D T A V Y Y C A A I T G T T D L W G R 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 V S A S V G D R V T I T C R A S Q G I N R R L A W Y Q Q K P G K A P K R L I Y A V S T L Q S G V P S R F N G S G S G T D F T L T V N N V Q P D D L A M Y F C L Q S N N Y P L T F G G G T K V E I K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen namegranulocyte-macrophage colony-stimulating factor
Antigen speciesHOMO SAPIENS
Antigen sequenceAPARSPSPSTQPWEHVNAIQEARRLLNLSRDTAAEMNETVEVISEMFDLQEPTCLQTRLELYKQGLRGSLTKLKGPLTMMASHYKQHCPPTPETSCATQIITFESFKENLKDFLLVIPFDCWEPVQE

CDR Sequences (chothia definition)
CDRH1DSAIRKY
CDRH2YASGS
CDRH3ITGTTDL
CDRL1RASQGINRRLA
CDRL2AVSTLQS
CDRL3LQSNNYPLT

Orientation Angles (from ABangle)
HL-60.58°
HC173.56°
HC2119.25°
LC1121.49°
LC281.71°
dc16.34Å
>   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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