Sars-Cov-2 Omicron Ba.1 Spike Glycoprotein in complex with Rabbit Monoclonal antibody 1H1 Fab in the Class 1 Conformation
PDB | 8h00 |
Species | ORYCTOLAGUS CUNICULUS |
Method | ELECTRON MICROSCOPY |
Resolution | 0Å |
Number of Fvs | 3 |
In complex | True |
Light chain type | Kappa |
Has constant region | False |
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Display options: |
This PDB has 3 Fv(s).
Fv Details | |
---|---|
Heavy chain | E |
Light chain | D |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV1 |
Species | ORYCTOLAGUS CUNICULUS |
In complex? | True |
scFv? | False |
Has constant domain? | False |
Numbered Sequences (chothia) |
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Heavy chain
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 | 52B | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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S | L | E | E | S | G | G | D | L | V | K | P | G | A | S | L | T | L | T | C | T | A | S | G | F | S | F | S | S | G | Y | D | M | C | W | V | R | Q | A | P | G | K | G | L | E | W | I | A | C | I | G | T | G | S | S | G | N | I | Y | Y | A | S | W | A | K | G | R | F | T | I | S | K | T | S | S | T | T | V | T | L | Q | M | T | S | L | T | A | A | D | T | A | T | Y | F | C | A | R | D | D | A | D | Y | A | G | P | D | Y | F | N | L | W | G | P | G | T | L | 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 | 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 | 95C | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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D | I | V | M | T | Q | T | P | A | S | V | S | E | P | V | G | G | T | V | T | I | K | C | Q | A | S | E | S | I | S | N | W | L | A | W | Y | Q | Q | K | P | G | Q | P | P | K | L | L | I | Y | A | A | F | T | L | A | S | G | V | P | S | R | F | K | G | S | G | S | G | T | Q | F | T | L | T | I | N | G | V | E | C | A | D | A | A | T | Y | Y | C | Q | Q | T | Y | S | S | R | D | V | D | N | V | F | G | G | G | T | E | V | V | V | K |
Antigen Details | |
---|---|
Antigen chains | A |
Antigen type | protein |
Antigen name | spike glycoprotein |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFSFSSGY |
CDRH2 | GTGSSGN |
CDRH3 | DDADYAGPDYFNL |
CDRL1 | QASESISNWLA |
CDRL2 | AAFTLAS |
CDRL3 | QQTYSSRDVDNV |
Orientation Angles (from ABangle) | |
---|---|
HL | -55.71° |
HC1 | 73.54° |
HC2 | 121.57° |
LC1 | 122.86° |
LC2 | 80.81° |
dc | 16.79Å |
Fv Details | |
---|---|
Heavy chain | G |
Light chain | F |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV1 |
Species | ORYCTOLAGUS CUNICULUS |
In complex? | True |
scFv? | False |
Has constant domain? | False |
Numbered Sequences (chothia) |
---|
Heavy chain
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 | 52B | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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S | L | E | E | S | G | G | D | L | V | K | P | G | A | S | L | T | L | T | C | T | A | S | G | F | S | F | S | S | G | Y | D | M | C | W | V | R | Q | A | P | G | K | G | L | E | W | I | A | C | I | G | T | G | S | S | G | N | I | Y | Y | A | S | W | A | K | G | R | F | T | I | S | K | T | S | S | T | T | V | T | L | Q | M | T | S | L | T | A | A | D | T | A | T | Y | F | C | A | R | D | D | A | D | Y | A | G | P | D | Y | F | N | L | W | G | P | G | T | L | 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 | 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 | 95C | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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D | I | V | M | T | Q | T | P | A | S | V | S | E | P | V | G | G | T | V | T | I | K | C | Q | A | S | E | S | I | S | N | W | L | A | W | Y | Q | Q | K | P | G | Q | P | P | K | L | L | I | Y | A | A | F | T | L | A | S | G | V | P | S | R | F | K | G | S | G | S | G | T | Q | F | T | L | T | I | N | G | V | E | C | A | D | A | A | T | Y | Y | C | Q | Q | T | Y | S | S | R | D | V | D | N | V | F | G | G | G | T | E | V | V | V | K |
Antigen Details | |
---|---|
Antigen chains | B |
Antigen type | protein |
Antigen name | spike glycoprotein |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFSFSSGY |
CDRH2 | GTGSSGN |
CDRH3 | DDADYAGPDYFNL |
CDRL1 | QASESISNWLA |
CDRL2 | AAFTLAS |
CDRL3 | QQTYSSRDVDNV |
Orientation Angles (from ABangle) | |
---|---|
HL | -55.84° |
HC1 | 73.76° |
HC2 | 121.12° |
LC1 | 122.18° |
LC2 | 80.65° |
dc | 16.78Å |
Fv Details | |
---|---|
Heavy chain | I |
Light chain | H |
Heavy subgroup | IGHV1 |
Light subgroup | IGKV1 |
Species | ORYCTOLAGUS CUNICULUS |
In complex? | True |
scFv? | False |
Has constant domain? | False |
Numbered Sequences (chothia) |
---|
Heavy chain
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 | 52B | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 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 | 101 | 102 | 103 | 104 | 105 | 106 | 107 | 108 | 109 | 110 | 111 | 112 | 113 |
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S | L | E | E | S | G | G | D | L | V | K | P | G | A | S | L | T | L | T | C | T | A | S | G | F | S | F | S | S | G | Y | D | M | C | W | V | R | Q | A | P | G | K | G | L | E | W | I | A | C | I | G | T | G | S | S | G | N | I | Y | Y | A | S | W | A | K | G | R | F | T | I | S | K | T | S | S | T | T | V | T | L | Q | M | T | S | L | T | A | A | D | T | A | T | Y | F | C | A | R | D | D | A | D | Y | A | G | P | D | Y | F | N | L | W | G | P | G | T | L | 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 | 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 | 95C | 96 | 97 | 98 | 99 | 100 | 101 | 102 | 103 | 104 | 105 | 106 | 107 |
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D | I | V | M | T | Q | T | P | A | S | V | S | E | P | V | G | G | T | V | T | I | K | C | Q | A | S | E | S | I | S | N | W | L | A | W | Y | Q | Q | K | P | G | Q | P | P | K | L | L | I | Y | A | A | F | T | L | A | S | G | V | P | S | R | F | K | G | S | G | S | G | T | Q | F | T | L | T | I | N | G | V | E | C | A | D | A | A | T | Y | Y | C | Q | Q | T | Y | S | S | R | D | V | D | N | V | F | G | G | G | T | E | V | V | V | K |
Antigen Details | |
---|---|
Antigen chains | C |
Antigen type | protein |
Antigen name | spike glycoprotein |
Antigen species | SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS2 |
Antigen sequence | MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSHGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDIFSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSHHHHHHHH |
CDR Sequences (chothia definition) | |
---|---|
CDRH1 | GFSFSSGY |
CDRH2 | GTGSSGN |
CDRH3 | DDADYAGPDYFNL |
CDRL1 | QASESISNWLA |
CDRL2 | AAFTLAS |
CDRL3 | QQTYSSRDVDNV |
Orientation Angles (from ABangle) | |
---|---|
HL | -55.66° |
HC1 | 73.66° |
HC2 | 121.76° |
LC1 | 122.98° |
LC2 | 80.68° |
dc | 16.76Å |
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]