|
|
eF-site ID
|
7kkk-C |
|
PDB Code
|
7kkk |
|
Chain
|
C |
|
click to enlarge
|
|
|
Title
|
SARS-CoV-2 Spike in complex with neutralizing nanobody Nb6 |
|
Classification
|
VIRAL PROTEIN/IMMUNE SYSTEM |
|
Compound
|
Spike glycoprotein |
|
Source
|
(7KKK) |
|
|
Sequence
|
C: |
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
|
|
|
Description
|
(1) |
SARS-CoV-2 spike glycoprotein, Synthetic nanobody Nb6
|
|
Functional site
|
|
|
1)
|
chain |
C |
| 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
|
|
|
2)
|
chain |
C |
| 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
|
|
|
3)
|
chain |
C |
| 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
|
|
|
4)
|
chain |
C |
| 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
|
|
|
5)
|
chain |
C |
| 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
|
|
|
6)
|
chain |
C |
| 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
|
|
|
7)
|
chain |
C |
| 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
|
|
|
8)
|
chain |
C |
| residue |
676 |
| type |
CARBOHYD |
| sequence |
T
|
| description |
O-linked (GlcNAc...) threonine; by host GALNT1 => ECO:0000269|PubMed:34732583
|
| source |
Swiss-Prot : SWS_FT_FI11
|
|
|
9)
|
chain |
C |
| 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
|
|
|
10)
|
chain |
C |
| residue |
323 |
| type |
CARBOHYD |
| sequence |
T
|
| description |
O-linked (GalNAc) threonine; by host => ECO:0000269|PubMed:32363391
|
| source |
Swiss-Prot : SWS_FT_FI8
|
|
|
11)
|
chain |
C |
| residue |
325 |
| type |
CARBOHYD |
| sequence |
S
|
| description |
O-linked (HexNAc...) serine; by host => ECO:0000269|PubMed:32363391
|
| source |
Swiss-Prot : SWS_FT_FI9
|
|
|
12)
|
chain |
C |
| 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
|
|
|
13)
|
chain |
C |
| 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
|
|
|
14)
|
chain |
C |
| 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
|
|
|
15)
|
chain |
C |
| 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
|
|
|
16)
|
chain |
C |
| 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
|
|
|
17)
|
chain |
C |
| 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 |
C |
| 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 |
C |
| 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 |
C |
| 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
|
|
|
|