Structure Viewer: 5d1z

>   Structure details

isdb Neat1 Bound By Clone D4-10

PDB5d1z
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution3.17Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
>   Structure visualisation
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>   Fv information

This PDB has 4 Fv(s).

>   D/C
Fv Details
Heavy chainD
Light chainC
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 31A 31B 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 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 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 I C T V S G G S I S S S S Y Y W G W I R Q T P E R N L E W I G I I Y F S G T T Y Y N P S L Q S R V S M S L D R S T N R F S L R L S S V T A A D T A I Y Y C A K P K S R D R G G P G D D Y F G M D V W G Q G I M 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 F L S A S V A D R V T I T C R A S Q A V R S S L A W Y Q Q K P G K A P Q L L I Y S A S T L E N G V S S R F S G S G P G T E F T L T I S S L Q P E D V G T Y Y C Q Q L N T Y P F T F G P G T K V E I K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen nameiron-regulated surface determinant protein b
Antigen speciesSTAPHYLOCOCCUS AUREUS (STRAIN MSSA476)
Antigen sequenceGPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVKPARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTKAVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT

CDR Sequences (chothia definition)
CDRH1GGSISSSSY
CDRH2YFSGT
CDRH3PKSRDRGGPGDDYFGMDV
CDRL1RASQAVRSSLA
CDRL2SASTLEN
CDRL3QQLNTYPFT

Orientation Angles (from ABangle)
HL-60.68°
HC174.08°
HC2118.54°
LC1119.15°
LC283.21°
dc16.23Å
>   F/E
Fv Details
Heavy chainF
Light chainE
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 31A 31B 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 99 100 100A 100B 100C 100D 100E 100F 100G 100H 100I 100J 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 I C T V S G G S I S S S S Y Y W G W I R Q T P E R N L E W I G I I Y F S G T T Y Y N P S L Q S R V S M S L D R S T N R F S L R L S S V T A A D T A I Y Y C A K P K S R D R G G P G D D Y F G M D V W G Q G I M 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 F L S A S V A D R V T I T C R A S Q A V R S S L A W Y Q Q K P G K A P Q L L I Y S A S T L E N G V S S R F S G S G P G T E F T L T I S S L Q P E D V G T Y Y C Q Q L N T Y P F T F G P G T K V E I K

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen nameiron-regulated surface determinant protein b
Antigen speciesSTAPHYLOCOCCUS AUREUS (STRAIN MSSA476)
Antigen sequenceGPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVKPARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTKAVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT

CDR Sequences (chothia definition)
CDRH1GGSISSSSY
CDRH2YFSGT
CDRH3PKSRDRGGPGDDYFGMDV
CDRL1RASQAVRSSLA
CDRL2SASTLEN
CDRL3QQLNTYPFT

Orientation Angles (from ABangle)
HL-61.48°
HC173.6°
HC2117.83°
LC1119.0°
LC282.43°
dc16.28Å
>   G/H
Fv Details
Heavy chainG
Light chainH
Heavy subgroupIGHV3
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 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 100C 100D 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G V V Q P G G S L R L S C A A S G F T F N K F W M N W V R Q A P G K G L E W V A D I Q V D G S E K N Y V D S V K G R F T I S R D N G K N S L Y L Q M N S L R A E D T G V Y Y C A R G R Y D Y W S G Y L S P 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 F L S A S V G D R V T I T C R A S Q G I T T Y L G W Y Q Q R P G K A P Q L L I Y A A S S L Q S G V P P 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 Q Q L N T Y P Y T F G P G T R L E I K

Antigen Details
Antigen chainsJ
Antigen typeprotein
Antigen nameiron-regulated surface determinant protein b
Antigen speciesSTAPHYLOCOCCUS AUREUS (STRAIN MSSA476)
Antigen sequenceGPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVKPARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTKAVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT

CDR Sequences (chothia definition)
CDRH1GFTFNKF
CDRH2QVDGSE
CDRH3GRYDYWSGYLSP
CDRL1RASQGITTYLG
CDRL2AASSLQS
CDRL3QQLNTYPYT

Orientation Angles (from ABangle)
HL-63.89°
HC170.81°
HC2121.81°
LC1121.41°
LC282.84°
dc16.23Å
>   B/A
Fv Details
Heavy chainB
Light chainA
Heavy subgroupIGHV3
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 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 100C 100D 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G G V V Q P G G S L R L S C A A S G F T F N K F W M N W V R Q A P G K G L E W V A D I Q V D G S E K N Y V D S V K G R F T I S R D N G K N S L Y L Q M N S L R A E D T G V Y Y C A R G R Y D Y W S G Y L S P 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 F L S A S V G D R V T I T C R A S Q G I T T Y L G W Y Q Q R P G K A P Q L L I Y A A S S L Q S G V P P 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 Q Q L N T Y P Y T F G P G T R L E I K

Antigen Details
Antigen chainsI
Antigen typeprotein
Antigen nameiron-regulated surface determinant protein b
Antigen speciesSTAPHYLOCOCCUS AUREUS (STRAIN MSSA476)
Antigen sequenceGPAKATNNTYPILNQELREAIKNPAIKDKDHSAPNSRPIDFEMKKKDGTQQFYHYASSVKPARVIFTDSKPEIELGLQSGQFWRKFEVYEGDKKLPIKLVSYDTVKDYAYIRFSVSNGTKAVKIVSSTHFNNKEEKYDYTLMEFAQPIYNSADKFKT

CDR Sequences (chothia definition)
CDRH1GFTFNKF
CDRH2QVDGSE
CDRH3GRYDYWSGYLSP
CDRL1RASQGITTYLG
CDRL2AASSLQS
CDRL3QQLNTYPYT

Orientation Angles (from ABangle)
HL-62.85°
HC171.09°
HC2121.28°
LC1121.08°
LC282.44°
dc16.19Å
>   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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