Structure Viewer: 4rzc

>   Structure details

Fv M6P-1 in complex with Mannose-6-Phosphate

PDB4rzc
SpeciesORYCTOLAGUS CUNICULUS
MethodX-RAY DIFFRACTION
Resolution2.723Å
Number of Fvs4
In complexTrue
Light chain typeKappa
Has constant regionFalse
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>   Fv information

This PDB has 4 Fv(s).

>   E/F
Fv Details
Heavy chainE
Light chainF
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 52B 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q S V K E S E G D L V K P G A S L T L T C K A S G F D F T W Y T M N W V R Q A P G K G L E W I A S I G A G V Y G S N Y Y A S W A K G R F T I S K A S S T T V T L Q M T S L T V A D T A T Y F C A R D G I N G G Y D I W G P G T L V T V S S

Light 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 30A 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
L V M T Q T E S P V S A A V G G T V T I K C Q S S Q S V Y N N R L A W Y Q Q K P G Q R P K L L I Y S A S T L A S G V P S R F K G S G S G T Q F T L T I S D L E W G D A A T Y Y C H G G Y R S N D D R Y A F S G G T E L E I L

Antigen Details
Antigen chainsE
Antigen typecarbohydrate
Antigen nameALPHA-D-MANNOSE-6-PHOSPHATE
Antigen speciesORYCTOLAGUS CUNICULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GFDFTWY
CDRH2GAGVYGS
CDRH3DGINGGYDI
CDRL1QSSQSVYNNRLA
CDRL2SASTLAS
CDRL3HGGYRSNDDRYA

Orientation Angles (from ABangle)
HL-54.55°
HC170.62°
HC2119.91°
LC1118.04°
LC282.87°
dc16.22Å
>   H/L
Fv Details
Heavy chainH
Light chainL
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 52B 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q S V K E S E G D L V K P G A S L T L T C K A S G F D F T W Y T M N W V R Q A P G K G L E W I A S I G A G V Y G S N Y Y A S W A K G R F T I S K A S S T T V T L Q M T S L T V A D T A T Y F C A R D G I N G G Y D I W G P G T L V T V S S

Light 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 30A 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
L V M T Q T E S P V S A A V G G T V T I K C Q S S Q S V Y N N R L A W Y Q Q K P G Q R P K L L I Y S A S T L A S G V P S R F K G S G S G T Q F T L T I S D L E W G D A A T Y Y C H G G Y R S N D D R Y A F S G G T E L E I L

Antigen Details
Antigen chainsH
Antigen typecarbohydrate
Antigen nameALPHA-D-MANNOSE-6-PHOSPHATE
Antigen speciesORYCTOLAGUS CUNICULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GFDFTWY
CDRH2GAGVYGS
CDRH3DGINGGYDI
CDRL1QSSQSVYNNRLA
CDRL2SASTLAS
CDRL3HGGYRSNDDRYA

Orientation Angles (from ABangle)
HL-54.91°
HC170.21°
HC2120.88°
LC1118.29°
LC282.48°
dc16.13Å
>   A/B
Fv Details
Heavy chainA
Light chainB
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 52B 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q S V K E S E G D L V K P G A S L T L T C K A S G F D F T W Y T M N W V R Q A P G K G L E W I A S I G A G V Y G S N Y Y A S W A K G R F T I S K A S S T T V T L Q M T S L T V A D T A T Y F C A R D G I N G G Y D I W G P G T L V T V S S

Light 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 30A 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
L V M T Q T E S P V S A A V G G T V T I K C Q S S Q S V Y N N R L A W Y Q Q K P G Q R P K L L I Y S A S T L A S G V P S R F K G S G S G T Q F T L T I S D L E W G D A A T Y Y C H G G Y R S N D D R Y A F S G G T E L E I L

Antigen Details
Antigen chainsA
Antigen typecarbohydrate
Antigen nameALPHA-D-MANNOSE-6-PHOSPHATE
Antigen speciesORYCTOLAGUS CUNICULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GFDFTWY
CDRH2GAGVYGS
CDRH3DGINGGYDI
CDRL1QSSQSVYNNRLA
CDRL2SASTLAS
CDRL3HGGYRSNDDRYA

Orientation Angles (from ABangle)
HL-54.53°
HC170.54°
HC2120.65°
LC1118.1°
LC282.77°
dc16.17Å
>   C/D
Fv Details
Heavy chainC
Light chainD
Heavy subgroupIGHV1
Light subgroupIGKV1
SpeciesORYCTOLAGUS CUNICULUS
In complex?True
scFv?False
Has constant domain?False

Numbered Sequences (chothia)

Heavy chain

1 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 52B 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 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 101 102 103 104 105 106 107 108 109 110 111 112 113
Q S V K E S E G D L V K P G A S L T L T C K A S G F D F T W Y T M N W V R Q A P G K G L E W I A S I G A G V Y G S N Y Y A S W A K G R F T I S K A S S T T V T L Q M T S L T V A D T A T Y F C A R D G I N G G Y D I W G P G T L V T V S S

Light 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 30A 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 95A 95B 95C 96 97 98 99 100 101 102 103 104 105 106 107
L V M T Q T E S P V S A A V G G T V T I K C Q S S Q S V Y N N R L A W Y Q Q K P G Q R P K L L I Y S A S T L A S G V P S R F K G S G S G T Q F T L T I S D L E W G D A A T Y Y C H G G Y R S N D D R Y A F S G G T E L E I L

Antigen Details
Antigen chainsC
Antigen typecarbohydrate
Antigen nameALPHA-D-MANNOSE-6-PHOSPHATE
Antigen speciesORYCTOLAGUS CUNICULUS
Antigen sequence

CDR Sequences (chothia definition)
CDRH1GFDFTWY
CDRH2GAGVYGS
CDRH3DGINGGYDI
CDRL1QSSQSVYNNRLA
CDRL2SASTLAS
CDRL3HGGYRSNDDRYA

Orientation Angles (from ABangle)
HL-54.17°
HC170.21°
HC2120.49°
LC1118.62°
LC282.66°
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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