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eF-site ID
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7kkl-A |
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PDB Code
|
7kkl |
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Chain
|
A |
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click to enlarge
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Title
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SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 |
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Classification
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VIRAL PROTEIN/IMMUNE SYSTEM |
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Compound
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Spike glycoprotein |
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Source
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(7KKL) |
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Sequence
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A: |
AYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFH
AIHDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQS
LLIVNNATNVVIKVCEFQFCNDPFLGVNCTFEYVSFKNLR
EFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLP
IGINITRFQTLLALHAAYYVGYLQPRTFLLKYNENGTITD
AVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIV
RFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSV
LYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEV
RQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGG
NYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFN
CYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP
KKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGR
DIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQ
VAVLYQDVNCTEVNVFQTRAGCLIGAEHVNNSYECDIPIG
AGICASYQTSQSIIAYTMSLGAENSVAYSNNSIAIPTNFT
ISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSF
CTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGG
FNFSQILPDPSKPSKRSFIEDLLFNKVTKFNGLTVLPPLL
TDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYR
FNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASAL
GKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLD
PPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLA
ATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHV
TYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVT
QRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPEL
DS
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Description
|
(1) |
SARS-CoV-2 spike glycoprotein, Synthetic nanobody mNb6
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Functional site
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|
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1)
|
chain |
A |
| residue |
323 |
| type |
CARBOHYD |
| sequence |
T
|
| description |
O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391
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| source |
Swiss-Prot : SWS_FT_FI8
|
|
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2)
|
chain |
A |
| residue |
325 |
| type |
CARBOHYD |
| sequence |
S
|
| description |
O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391
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| source |
Swiss-Prot : SWS_FT_FI9
|
|
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3)
|
chain |
A |
| residue |
603 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI10
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|
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4)
|
chain |
A |
| residue |
676 |
| type |
CARBOHYD |
| sequence |
T
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| description |
O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583
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| source |
Swiss-Prot : SWS_FT_FI11
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|
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5)
|
chain |
A |
| residue |
1134 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI12
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|
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6)
|
chain |
A |
| residue |
815 |
| type |
SITE |
| sequence |
R
|
| description |
Cleavage; by host TMPRSS2 or CTSL => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32703818, ECO:0000269|PubMed:34159616
|
| source |
Swiss-Prot : SWS_FT_FI2
|
|
|
7)
|
chain |
A |
| residue |
61 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI4
|
|
|
8)
|
chain |
A |
| residue |
122 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI4
|
|
|
9)
|
chain |
A |
| residue |
717 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI4
|
|
|
10)
|
chain |
A |
| residue |
801 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI4
|
|
|
11)
|
chain |
A |
| residue |
1074 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (hybrid) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI4
|
|
|
12)
|
chain |
A |
| residue |
343 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
13)
|
chain |
A |
| residue |
616 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
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14)
|
chain |
A |
| residue |
657 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
15)
|
chain |
A |
| residue |
1098 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
16)
|
chain |
A |
| residue |
331 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
17)
|
chain |
A |
| residue |
165 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
18)
|
chain |
A |
| residue |
282 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (complex) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI6
|
|
|
19)
|
chain |
A |
| residue |
234 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI7
|
|
|
20)
|
chain |
A |
| residue |
709 |
| type |
CARBOHYD |
| sequence |
N
|
| description |
N-linked (GlcNAc...) (high mannose) asparagine; by host => ECO:0000255|HAMAP-Rule:MF_04099, ECO:0000269|PubMed:32155444, ECO:0000269|PubMed:32363391, ECO:0000269|PubMed:32366695, ECO:0000269|PubMed:32979942
|
| source |
Swiss-Prot : SWS_FT_FI7
|
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