Plasmodium Vivax Reticulocyte Binding Protein 2B (Pvrbp2B) Bound to Human Monoclonal antibody 273264
PDB | 6wtu |
Species | HOMO SAPIENS |
Method | X-RAY DIFFRACTION |
Resolution | 2.55Å |
Number of Fvs | 4 |
In complex | True |
Light chain type | Lambda |
Has constant region | True |
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Display options: |
This PDB has 4 Fv(s).
Fv Details | |
---|---|
Heavy chain | H |
Light chain | I |
Heavy subgroup | IGHV3 |
Light subgroup | IGLV3 |
Species | HOMO SAPIENS |
In complex? | True |
scFv? | False |
Has constant domain? | True |
Numbered Sequences (chothia) |
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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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | L | E | S | G | G | G | L | V | R | P | G | G | S | Q | R | L | S | C | A | A | S | G | F | T | F | T | P | Y | A | M | T | W | V | R | Q | A | P | G | K | G | L | E | W | L | S | T | I | S | G | S | G | G | S | T | S | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | N | S | K | N | I | L | Y | L | Q | M | D | S | L | R | A | E | D | T | A | L | Y | Y | C | T | K | D | K | D | E | Y | T | F | G | H | N | A | F | D | V | W | G | R | G | T | M | V | T | V | S | S |
Light chain
1 | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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S | Y | E | L | T | Q | A | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | D | N | I | G | R | T | S | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | I | F | Y | D | N | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | M | A | T | L | S | I | S | R | V | E | V | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | N | N | D | H | P | V | F | G | G | G | T | K | L | T | V | V |
Antigen Details | |
---|---|
Antigen chains | G |
Antigen type | protein |
Antigen name | reticulocyte binding protein 2b |
Antigen species | PLASMODIUM VIVAX (STRAIN SALVADOR I) |
Antigen sequence | GAMGSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFTFTPY |
CDRH2 | SGSGGS |
CDRH3 | DKDEYTFGHNAFDV |
CDRL1 | GGDNIGRTSVH |
CDRL2 | YDNDRPS |
CDRL3 | QVWDSNNDHPV |
Orientation Angles (from ABangle) | |
---|---|
HL | -56.38° |
HC1 | 70.67° |
HC2 | 117.88° |
LC1 | 119.55° |
LC2 | 82.2° |
dc | 16.47Å |
Fv Details | |
---|---|
Heavy chain | K |
Light chain | L |
Heavy subgroup | IGHV3 |
Light subgroup | IGLV3 |
Species | HOMO 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | L | E | S | G | G | G | L | V | R | P | G | G | S | Q | R | L | S | C | A | A | S | G | F | T | F | T | P | Y | A | M | T | W | V | R | Q | A | P | G | K | G | L | E | W | L | S | T | I | S | G | S | G | G | S | T | S | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | N | S | K | N | I | L | Y | L | Q | M | D | S | L | R | A | E | D | T | A | L | Y | Y | C | T | K | D | K | D | E | Y | T | F | G | H | N | A | F | D | V | W | G | R | G | T | M | V | T | V | S | S |
Light chain
1 | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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S | Y | E | L | T | Q | A | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | D | N | I | G | R | T | S | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | I | F | Y | D | N | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | M | A | T | L | S | I | S | R | V | E | V | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | N | N | D | H | P | V | F | G | G | G | T | K | L | T | V | V |
Antigen Details | |
---|---|
Antigen chains | J |
Antigen type | protein |
Antigen name | reticulocyte binding protein 2b |
Antigen species | PLASMODIUM VIVAX (STRAIN SALVADOR I) |
Antigen sequence | GAMGSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFTFTPY |
CDRH2 | SGSGGS |
CDRH3 | DKDEYTFGHNAFDV |
CDRL1 | GGDNIGRTSVH |
CDRL2 | YDNDRPS |
CDRL3 | QVWDSNNDHPV |
Orientation Angles (from ABangle) | |
---|---|
HL | -57.04° |
HC1 | 70.7° |
HC2 | 117.96° |
LC1 | 119.26° |
LC2 | 82.29° |
dc | 16.47Å |
Fv Details | |
---|---|
Heavy chain | E |
Light chain | F |
Heavy subgroup | IGHV3 |
Light subgroup | IGLV3 |
Species | HOMO 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | L | E | S | G | G | G | L | V | R | P | G | G | S | Q | R | L | S | C | A | A | S | G | F | T | F | T | P | Y | A | M | T | W | V | R | Q | A | P | G | K | G | L | E | W | L | S | T | I | S | G | S | G | G | S | T | S | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | N | S | K | N | I | L | Y | L | Q | M | D | S | L | R | A | E | D | T | A | L | Y | Y | C | T | K | D | K | D | E | Y | T | F | G | H | N | A | F | D | V | W | G | R | G | T | M | V | T | V | S | S |
Light chain
1 | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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S | Y | E | L | T | Q | A | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | D | N | I | G | R | T | S | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | I | F | Y | D | N | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | M | A | T | L | S | I | S | R | V | E | V | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | N | N | D | H | P | V | F | G | G | G | T | K | L | T | V | V |
Antigen Details | |
---|---|
Antigen chains | D |
Antigen type | protein |
Antigen name | reticulocyte binding protein 2b |
Antigen species | PLASMODIUM VIVAX (STRAIN SALVADOR I) |
Antigen sequence | GAMGSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFTFTPY |
CDRH2 | SGSGGS |
CDRH3 | DKDEYTFGHNAFDV |
CDRL1 | GGDNIGRTSVH |
CDRL2 | YDNDRPS |
CDRL3 | QVWDSNNDHPV |
Orientation Angles (from ABangle) | |
---|---|
HL | -57.13° |
HC1 | 71.28° |
HC2 | 117.83° |
LC1 | 120.89° |
LC2 | 82.28° |
dc | 16.2Å |
Fv Details | |
---|---|
Heavy chain | B |
Light chain | C |
Heavy subgroup | IGHV3 |
Light subgroup | IGLV3 |
Species | HOMO 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | Q | L | L | E | S | G | G | G | L | V | R | P | G | G | S | Q | R | L | S | C | A | A | S | G | F | T | F | T | P | Y | A | M | T | W | V | R | Q | A | P | G | K | G | L | E | W | L | S | T | I | S | G | S | G | G | S | T | S | Y | A | D | S | V | K | G | R | F | T | I | S | R | D | N | S | K | N | I | L | Y | L | Q | M | D | S | L | R | A | E | D | T | A | L | Y | Y | C | T | K | D | K | D | E | Y | T | F | G | H | N | A | F | D | V | W | G | R | G | T | M | V | T | V | S | S |
Light chain
1 | 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 | 95A | 95B | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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S | Y | E | L | T | Q | A | P | S | V | S | V | A | P | G | Q | T | A | R | I | T | C | G | G | D | N | I | G | R | T | S | V | H | W | Y | Q | Q | K | P | G | Q | A | P | V | L | V | I | F | Y | D | N | D | R | P | S | G | I | P | E | R | F | S | G | S | N | S | G | N | M | A | T | L | S | I | S | R | V | E | V | G | D | E | A | D | Y | Y | C | Q | V | W | D | S | N | N | D | H | P | V | F | G | G | G | T | K | L | T | V | V |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | reticulocyte binding protein 2b |
Antigen species | PLASMODIUM VIVAX (STRAIN SALVADOR I) |
Antigen sequence | GAMGSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFTFTPY |
CDRH2 | SGSGGS |
CDRH3 | DKDEYTFGHNAFDV |
CDRL1 | GGDNIGRTSVH |
CDRL2 | YDNDRPS |
CDRL3 | QVWDSNNDHPV |
Orientation Angles (from ABangle) | |
---|---|
HL | -57.01° |
HC1 | 70.99° |
HC2 | 118.14° |
LC1 | 120.34° |
LC2 | 82.41° |
dc | 16.28Å |
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]