Structure Viewer: 3mls

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Crystal Structure of anti-Hiv-1 V3 Mab 2557 Fab in complex with a Hiv-1 Gp120 V3 Mimotope

PDB3mls
SpeciesHOMO SAPIENS
MethodX-RAY DIFFRACTION
Resolution2.5Å
Number of Fvs4
In complexTrue
Light chain typeLambda
Has constant regionTrue
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>   Fv information

This PDB has 4 Fv(s).

>   J/N
Fv Details
Heavy chainJ
Light chainN
Heavy subgroupIGHV5
Light subgroupIGLV3
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 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G E V K Q P G Q S L K I S C K S S G Y N F L D S W I G W V R Q I P G K G L E W I G I I Y P D D S D A H Y S P S F E G Q V T M S V D K S I S T A Y L Q W T T L Q A S D T G K Y F C T R L Y L F E G A Q S S N A F D L W G Q G T M I L V S S

Light chain

2 3 4 5 6 7 8 9 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
Y D L T Q P P S V S V S P G Q T A S I S C S G D K L D D K Y V S W Y Y Q R P G Q S P V L L M Y Q D F K R P S G I P E R L S G S K S G K T A T L T I S G T Q S L D E G D Y Y C Q A W D A S T G V S G G G T K L T V L

Antigen Details
Antigen chainsR
Antigen typepeptide
Antigen namerationally designed v3 mimotope
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequenceACQAFYASSPRKSIHIGACA

CDR Sequences (chothia definition)
CDRH1GYNFLDS
CDRH2YPDDSD
CDRH3LYLFEGAQSSNAFDL
CDRL1SGDKLDDKYVS
CDRL2QDFKRPS
CDRL3QAWDASTGV

Orientation Angles (from ABangle)
HL-56.2°
HC170.94°
HC2116.83°
LC1122.1°
LC282.04°
dc16.36Å
>   I/M
Fv Details
Heavy chainI
Light chainM
Heavy subgroupIGHV5
Light subgroupIGLV3
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 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G E V K Q P G Q S L K I S C K S S G Y N F L D S W I G W V R Q I P G K G L E W I G I I Y P D D S D A H Y S P S F E G Q V T M S V D K S I S T A Y L Q W T T L Q A S D T G K Y F C T R L Y L F E G A Q S S N A F D L W G Q G T M I L V S S

Light chain

2 3 4 5 6 7 8 9 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
Y D L T Q P P S V S V S P G Q T A S I S C S G D K L D D K Y V S W Y Y Q R P G Q S P V L L M Y Q D F K R P S G I P E R L S G S K S G K T A T L T I S G T Q S L D E G D Y Y C Q A W D A S T G V S G G G T K L T V L

Antigen Details
Antigen chainsQ
Antigen typepeptide
Antigen namerationally designed v3 mimotope
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequenceACQAFYASSPRKSIHIGACA

CDR Sequences (chothia definition)
CDRH1GYNFLDS
CDRH2YPDDSD
CDRH3LYLFEGAQSSNAFDL
CDRL1SGDKLDDKYVS
CDRL2QDFKRPS
CDRL3QAWDASTGV

Orientation Angles (from ABangle)
HL-57.23°
HC170.69°
HC2116.74°
LC1122.51°
LC282.07°
dc16.44Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV5
Light subgroupIGLV3
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 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G E V K Q P G Q S L K I S C K S S G Y N F L D S W I G W V R Q I P G K G L E W I G I I Y P D D S D A H Y S P S F E G Q V T M S V D K S I S T A Y L Q W T T L Q A S D T G K Y F C T R L Y L F E G A Q S S N A F D L W G Q G T M I L V S S

Light chain

2 3 4 5 6 7 8 9 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
Y D L T Q P P S V S V S P G Q T A S I S C S G D K L D D K Y V S W Y Y Q R P G Q S P V L L M Y Q D F K R P S G I P E R L S G S K S G K T A T L T I S G T Q S L D E G D Y Y C Q A W D A S T G V S G G G T K L T V L

Antigen Details
Antigen chainsP
Antigen typepeptide
Antigen namerationally designed v3 mimotope
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequenceACQAFYASSPRKSIHIGACA

CDR Sequences (chothia definition)
CDRH1GYNFLDS
CDRH2YPDDSD
CDRH3LYLFEGAQSSNAFDL
CDRL1SGDKLDDKYVS
CDRL2QDFKRPS
CDRL3QAWDASTGV

Orientation Angles (from ABangle)
HL-58.76°
HC170.29°
HC2116.49°
LC1121.76°
LC281.05°
dc16.51Å
>   K/O
Fv Details
Heavy chainK
Light chainO
Heavy subgroupIGHV5
Light subgroupIGLV3
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 100E 100F 100G 101 102 103 104 105 106 107 108 109 110 111 112 113
E V Q L V E S G G E V K Q P G Q S L K I S C K S S G Y N F L D S W I G W V R Q I P G K G L E W I G I I Y P D D S D A H Y S P S F E G Q V T M S V D K S I S T A Y L Q W T T L Q A S D T G K Y F C T R L Y L F E G A Q S S N A F D L W G Q G T M I L V S S

Light chain

2 3 4 5 6 7 8 9 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
Y D L T Q P P S V S V S P G Q T A S I S C S G D K L D D K Y V S W Y Y Q R P G Q S P V L L M Y Q D F K R P S G I P E R L S G S K S G K T A T L T I S G T Q S L D E G D Y Y C Q A W D A S T G V S G G G T K L T V L

Antigen Details
Antigen chainsS
Antigen typepeptide
Antigen namerationally designed v3 mimotope
Antigen speciesSYNTHETIC CONSTRUCT
Antigen sequenceACQAFYASSPRKSIHIGACA

CDR Sequences (chothia definition)
CDRH1GYNFLDS
CDRH2YPDDSD
CDRH3LYLFEGAQSSNAFDL
CDRL1SGDKLDDKYVS
CDRL2QDFKRPS
CDRL3QAWDASTGV

Orientation Angles (from ABangle)
HL-56.48°
HC171.1°
HC2116.44°
LC1122.02°
LC281.72°
dc16.34Å
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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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