Structure Viewer: 1nd0

>   Structure details

Cationic Cyclization antibody 4C6 complex with Transition State analog

PDB1nd0
SpeciesMUS MUSCULUS
MethodX-RAY DIFFRACTION
Resolution2.45Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   B/A
Fv Details
Heavy chainB
Light chainA
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 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
V Q L Q Q S G P G L V K P S Q S L S L T C T V T G Y S I T S D F A W N W I R Q F P G N K L E W M G Y I N Y S G F T S H N P S L K S R I S I T R D T S K N Q F F L Q L N S V T T E D T A T Y Y C A G L L W Y D G G A G S W G Q G T L V T V 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 30A 30B 30C 30D 30E 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 V V M T Q S P K T I S V T I G Q P A S I S C K S S Q R L L N S N G K T F L N W L L Q R P G Q S P K R L I Y L G T K L D S G V P D R F T G S G S G T D F T L K I S R V E A E D L G V Y Y C W Q G T H F P Y T F G G G T K L E I K

Antigen Details
Antigen chainsA
Antigen typeHapten
Antigen name(1S,4S)-4-[DIMETHYL(PHENYL)SILYL]-1-METHYLPIPERIDINE 1-OXIDE
Antigen speciesMUS MUSCULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GYSITSDF
CDRH2NYSGF
CDRH3LLWYDGGAGS
CDRL1KSSQRLLNSNGKTFLN
CDRL2LGTKLDS
CDRL3WQGTHFPYT

Orientation Angles (from ABangle)
HL-62.75°
HC169.75°
HC2116.8°
LC1120.04°
LC283.62°
dc16.24Å
>   H/G
Fv Details
Heavy chainH
Light chainG
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 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
V Q L Q Q S G P G L V K P S Q S L S L T C T V T G Y S I T S D F A W N W I R Q F P G N K L E W M G Y I N Y S G F T S H N P S L K S R I S I T R D T S K N Q F F L Q L N S V T T E D T A T Y Y C A G L L W Y D G G A G S W G Q G T L V T V 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 30A 30B 30C 30D 30E 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 V V M T Q S P K T I S V T I G Q P A S I S C K S S Q R L L N S N G K T F L N W L L Q R P G Q S P K R L I Y L G T K L D S G V P D R F T G S G S G T D F T L K I S R V E A E D L G V Y Y C W Q G T H F P Y T F G G G T K L E I K

Antigen Details
Antigen chainsG
Antigen typeHapten
Antigen name(1S,4S)-4-[DIMETHYL(PHENYL)SILYL]-1-METHYLPIPERIDINE 1-OXIDE
Antigen speciesMUS MUSCULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GYSITSDF
CDRH2NYSGF
CDRH3LLWYDGGAGS
CDRL1KSSQRLLNSNGKTFLN
CDRL2LGTKLDS
CDRL3WQGTHFPYT

Orientation Angles (from ABangle)
HL-62.24°
HC169.46°
HC2116.66°
LC1120.33°
LC284.23°
dc16.33Å
>   D/C
Fv Details
Heavy chainD
Light chainC
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 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
V Q L Q Q S G P G L V K P S Q S L S L T C T V T G Y S I T S D F A W N W I R Q F P G N K L E W M G Y I N Y S G F T S H N P S L K S R I S I T R D T S K N Q F F L Q L N S V T T E D T A T Y Y C A G L L W Y D G G A G S W G Q G T L V T V 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 30A 30B 30C 30D 30E 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 V V M T Q S P K T I S V T I G Q P A S I S C K S S Q R L L N S N G K T F L N W L L Q R P G Q S P K R L I Y L G T K L D S G V P D R F T G S G S G T D F T L K I S R V E A E D L G V Y Y C W Q G T H F P Y T F G G G T K L E I K

Antigen Details
Antigen chainsC
Antigen typeHapten
Antigen name(1S,4S)-4-[DIMETHYL(PHENYL)SILYL]-1-METHYLPIPERIDINE 1-OXIDE
Antigen speciesMUS MUSCULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GYSITSDF
CDRH2NYSGF
CDRH3LLWYDGGAGS
CDRL1KSSQRLLNSNGKTFLN
CDRL2LGTKLDS
CDRL3WQGTHFPYT

Orientation Angles (from ABangle)
HL-62.31°
HC169.67°
HC2116.75°
LC1120.08°
LC284.09°
dc16.33Å
>   F/E
Fv Details
Heavy chainF
Light chainE
Heavy subgroupIGHV3
Light subgroupIGKV1
SpeciesMUS MUSCULUS
In complex?True
scFv?False
Has constant domain?True

Numbered Sequences (chothia)

Heavy chain

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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 52A 53 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
V Q L Q Q S G P G L V K P S Q S L S L T C T V T G Y S I T S D F A W N W I R Q F P G N K L E W M G Y I N Y S G F T S H N P S L K S R I S I T R D T S K N Q F F L Q L N S V T T E D T A T Y Y C A G L L W Y D G G A G S W G Q G T L V T V 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 30A 30B 30C 30D 30E 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 V V M T Q S P K T I S V T I G Q P A S I S C K S S Q R L L N S N G K T F L N W L L Q R P G Q S P K R L I Y L G T K L D S G V P D R F T G S G S G T D F T L K I S R V E A E D L G V Y Y C W Q G T H F P Y T F G G G T K L E I K

Antigen Details
Antigen chainsE
Antigen typeHapten
Antigen name(1S,4S)-4-[DIMETHYL(PHENYL)SILYL]-1-METHYLPIPERIDINE 1-OXIDE
Antigen speciesMUS MUSCULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GYSITSDF
CDRH2NYSGF
CDRH3LLWYDGGAGS
CDRL1KSSQRLLNSNGKTFLN
CDRL2LGTKLDS
CDRL3WQGTHFPYT

Orientation Angles (from ABangle)
HL-62.72°
HC170.27°
HC2116.76°
LC1119.75°
LC283.64°
dc16.26Å
>   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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