Structure Viewer: 5vjq

>   Structure details

complex Between Hyhel10 Fab Fragment Heavy Chain Mutant (I29F, S52T, Y53F) and Pekin Duck Egg Lysozyme isoform I (Del-I)

PDB5vjq
SpeciesMUS MUSCULUS
MethodX-RAY DIFFRACTION
Resolution1.9Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV3
Light subgroupIGKV5
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 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 97 101 102 103 104 105 106 107 108 109 110 111 112 113
D V Q L Q E S G P S L V K P S Q T L S L T C S V T G D S F T S D Y W S W I R K F P G N R L E Y M G Y V T F S G S T Y Y N P S L K S R I S I T R D T S K N Q Y Y L D L N S V T T E D T A T Y Y C A N W D G D Y W G Q G T L V T V S A

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

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen namelysozyme
Antigen speciesANAS PLATYRHYNCHOS
Antigen sequenceKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKWIRGCRL

CDR Sequences (chothia definition)
CDRH1GDSFTSD
CDRH2TFSGS
CDRH3WDGDY
CDRL1RASQSIGNNLH
CDRL2YASQSIS
CDRL3QQSNSWPYT

Orientation Angles (from ABangle)
HL-62.0°
HC171.45°
HC2117.71°
LC1119.16°
LC282.66°
dc16.25Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV3
Light subgroupIGKV5
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 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 97 101 102 103 104 105 106 107 108 109 110 111 112 113
D V Q L Q E S G P S L V K P S Q T L S L T C S V T G D S F T S D Y W S W I R K F P G N R L E Y M G Y V T F S G S T Y Y N P S L K S R I S I T R D T S K N Q Y Y L D L N S V T T E D T A T Y Y C A N W D G D Y W G Q G T L V T V S A

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

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen namelysozyme
Antigen speciesANAS PLATYRHYNCHOS
Antigen sequenceKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKWIRGCRL

CDR Sequences (chothia definition)
CDRH1GDSFTSD
CDRH2TFSGS
CDRH3WDGDY
CDRL1RASQSIGNNLH
CDRL2YASQSIS
CDRL3QQSNSWPYT

Orientation Angles (from ABangle)
HL-62.15°
HC170.83°
HC2117.7°
LC1120.43°
LC283.98°
dc16.26Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV3
Light subgroupIGKV5
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 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 97 101 102 103 104 105 106 107 108 109 110 111 112 113
D V Q L Q E S G P S L V K P S Q T L S L T C S V T G D S F T S D Y W S W I R K F P G N R L E Y M G Y V T F S G S T Y Y N P S L K S R I S I T R D T S K N Q Y Y L D L N S V T T E D T A T Y Y C A N W D G D Y W G Q G T L V T V S A

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

Antigen Details
Antigen chainsL
Antigen typeprotein
Antigen namelysozyme
Antigen speciesANAS PLATYRHYNCHOS
Antigen sequenceKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKWIRGCRL

CDR Sequences (chothia definition)
CDRH1GDSFTSD
CDRH2TFSGS
CDRH3WDGDY
CDRL1RASQSIGNNLH
CDRL2YASQSIS
CDRL3QQSNSWPYT

Orientation Angles (from ABangle)
HL-61.09°
HC172.44°
HC2117.77°
LC1120.84°
LC283.48°
dc15.99Å
>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV3
Light subgroupIGKV5
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 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 97 101 102 103 104 105 106 107 108 109 110 111 112 113
D V Q L Q E S G P S L V K P S Q T L S L T C S V T G D S F T S D Y W S W I R K F P G N R L E Y M G Y V T F S G S T Y Y N P S L K S R I S I T R D T S K N Q Y Y L D L N S V T T E D T A T Y Y C A N W D G D Y W G Q G T L V T V S A

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

Antigen Details
Antigen chainsK
Antigen typeprotein
Antigen namelysozyme
Antigen speciesANAS PLATYRHYNCHOS
Antigen sequenceKVYSRCELAAAMKRLGLDNYRGYSLGNWVCAANYESSFNTQATNRNTDGSTDYGILQINSRWWCDDGKTPGSKNACGIPCSVLLRSDITEAVRCAKRIVSDGNGMNAWVAWRNRCRGTDVSKWIRGCRL

CDR Sequences (chothia definition)
CDRH1GDSFTSD
CDRH2TFSGS
CDRH3WDGDY
CDRL1RASQSIGNNLH
CDRL2YASQSIS
CDRL3QQSNSWPYT

Orientation Angles (from ABangle)
HL-61.11°
HC171.45°
HC2117.3°
LC1120.05°
LC283.79°
dc16.19Å
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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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