Structure of Clc-Ec1 Deltanc Construct in 20Mm Bromide
PDB | 4kk6 |
Species | MUS MUSCULUS |
Method | X-RAY DIFFRACTION |
Resolution | 3.183Å |
Number of Fvs | 2 |
In complex | True |
Light chain type | Kappa |
Has constant region | True |
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Display options: |
This PDB has 2 Fv(s).
Fv Details | |
---|---|
Heavy chain | E |
Light chain | F |
Heavy subgroup | IGHV4 |
Light subgroup | IGKV4 |
Species | MUS MUSCULUS |
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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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E | V | R | L | L | E | S | G | G | G | L | V | Q | P | G | G | S | L | K | L | S | C | A | A | S | G | F | D | Y | S | R | Y | W | M | S | W | V | R | Q | A | P | G | K | G | L | K | W | I | G | E | I | N | P | V | S | S | T | I | N | Y | T | P | S | L | K | D | K | F | I | I | S | R | D | N | A | K | D | T | L | Y | L | Q | I | S | K | V | R | S | E | D | T | A | L | Y | Y | C | A | R | L | Y | Y | G | Y | G | Y | W | Y | F | D | V | W | G | A | G | T | T | 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 | 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 |
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D | I | V | L | T | Q | S | P | A | I | M | S | A | A | P | G | D | K | V | T | M | T | C | S | A | S | S | S | V | S | Y | I | H | W | Y | Q | Q | K | S | G | T | S | P | K | R | W | I | Y | D | T | S | K | L | T | S | G | V | P | V | R | F | S | G | S | G | S | G | T | S | Y | S | L | T | I | N | T | M | E | A | E | D | A | A | T | Y | Y | C | Q | Q | W | S | S | H | P | Q | T | F | G | G | G | T | K | L | E | I |
Antigen Details | |
---|---|
Antigen chains | B |
Antigen type | protein |
Antigen name | h(+)/cl(-) exchange transporter clca |
Antigen species | ESCHERICHIA COLI |
Antigen sequence | MRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLSDAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGGGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEAEQK |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFDYSRY |
CDRH2 | NPVSST |
CDRH3 | LYYGYGYWYFDV |
CDRL1 | SASSSVSYIH |
CDRL2 | DTSKLTS |
CDRL3 | QQWSSHPQT |
Orientation Angles (from ABangle) | |
---|---|
HL | -61.82° |
HC1 | 73.66° |
HC2 | 117.09° |
LC1 | 117.41° |
LC2 | 80.62° |
dc | 16.3Å |
Fv Details | |
---|---|
Heavy chain | C |
Light chain | D |
Heavy subgroup | IGHV4 |
Light subgroup | IGKV4 |
Species | MUS MUSCULUS |
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 |
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E | V | R | L | L | E | S | G | G | G | L | V | Q | P | G | G | S | L | K | L | S | C | A | A | S | G | F | D | Y | S | R | Y | W | M | S | W | V | R | Q | A | P | G | K | G | L | K | W | I | G | E | I | N | P | V | S | S | T | I | N | Y | T | P | S | L | K | D | K | F | I | I | S | R | D | N | A | K | D | T | L | Y | L | Q | I | S | K | V | R | S | E | D | T | A | L | Y | Y | C | A | R | L | Y | Y | G | Y | G | Y | W | Y | F | D | V | W | G | A | G | T | T | 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 | 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 |
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D | I | V | L | T | Q | S | P | A | I | M | S | A | A | P | G | D | K | V | T | M | T | C | S | A | S | S | S | V | S | Y | I | H | W | Y | Q | Q | K | S | G | T | S | P | K | R | W | I | Y | D | T | S | K | L | T | S | G | V | P | V | R | F | S | G | S | G | S | G | T | S | Y | S | L | T | I | N | T | M | E | A | E | D | A | A | T | Y | Y | C | Q | Q | W | S | S | H | P | Q | T | F | G | G | G | T | K | L | E | I |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | h(+)/cl(-) exchange transporter clca |
Antigen species | ESCHERICHIA COLI |
Antigen sequence | MRRRQLIRQLLERDKTPLAILFMAAVVGTLVGLAAVAFDKGVAWLQNQRMGALVHTADNYPLLLTVAFLCSAVLAMFGYFLVRKYAPEAGGSGIPEIEGALEDQRPVRWWRVLPVKFFGGLGTLGGGMVLGREGPTVQIGGNIGRMVLDIFRLKGDEARHTLLATGAAAGLAAAFNAPLAGILFIIEEMRPQFRYTLISIKAVFIGVIMSTIMYRIFNHEVALIDVGKLSDAPLNTLWLYLILGIIFGIFGPIFNKWVLGMQDLLHRVHGGNITKWVLMGGAIGGLCGLLGFVAPATSGGGFNLIPIATAGNFSMGMLVFIFVARVITTLLCFSSGAPGGIFAPMLALGTVLGTAFGMVAVELFPQYHLEAGTFAIAGMGALLAASIRAPLTGIILVLEMTDNYQLILPMIITGLGATLLAQFTGGKPLYSAILARTLAKQEAEQK |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFDYSRY |
CDRH2 | NPVSST |
CDRH3 | LYYGYGYWYFDV |
CDRL1 | SASSSVSYIH |
CDRL2 | DTSKLTS |
CDRL3 | QQWSSHPQT |
Orientation Angles (from ABangle) | |
---|---|
HL | -64.67° |
HC1 | 73.11° |
HC2 | 115.23° |
LC1 | 116.99° |
LC2 | 79.66° |
dc | 15.98Å |
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]