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3KBH
Asym. Unit
Info
Asym.Unit (460 KB)
Biol.Unit 1 (228 KB)
Biol.Unit 2 (227 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NL63 RESPIRATORY CORONAVIRUS RECEPTOR-BINDING DOMAIN COMPLEXED WITH ITS HUMAN RECEPTOR
Authors
:
K. Wu, W. Li, G. Peng, F. Li
Date
:
20 Oct 09 (Deposition) - 15 Dec 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.31
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,C,E,G (1x)
Biol. Unit 2: B,D,F,H (1x)
Keywords
:
Beta Sandwich, Envelope Protein, Fusion Protein, Glycoprotein, Host- Virus Interaction, Membrane, Transmembrane, Virion, Virulence, Carboxypeptidase, Cell Membrane, Chloride, Metal-Binding, Metalloprotease, Protease, Secreted, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
K. Wu, W. Li, G. Peng, F. Li
Crystal Structure Of Nl63 Respiratory Coronavirus Receptor-Binding Domain Complexed With Its Human Receptor.
Proc. Natl. Acad. Sci. Usa V. 106 19970 2009
[
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Hetero Components
(1, 16)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
1f: N-ACETYL-D-GLUCOSAMINE (NAGf)
1g: N-ACETYL-D-GLUCOSAMINE (NAGg)
1h: N-ACETYL-D-GLUCOSAMINE (NAGh)
1i: N-ACETYL-D-GLUCOSAMINE (NAGi)
1j: N-ACETYL-D-GLUCOSAMINE (NAGj)
1k: N-ACETYL-D-GLUCOSAMINE (NAGk)
1l: N-ACETYL-D-GLUCOSAMINE (NAGl)
1m: N-ACETYL-D-GLUCOSAMINE (NAGm)
1n: N-ACETYL-D-GLUCOSAMINE (NAGn)
1o: N-ACETYL-D-GLUCOSAMINE (NAGo)
1p: N-ACETYL-D-GLUCOSAMINE (NAGp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
16
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:26 , ASN A:90
BINDING SITE FOR RESIDUE NAG A 800
02
AC2
SOFTWARE
SER A:420 , ASN A:546
BINDING SITE FOR RESIDUE NAG A 801
03
AC3
SOFTWARE
LYS D:131 , ASP E:484 , ASN E:486
BINDING SITE FOR RESIDUE NAG E 1486
04
AC4
SOFTWARE
ASN E:510 , ASN E:512
BINDING SITE FOR RESIDUE NAG E 1512
05
AC5
SOFTWARE
LYS B:26 , ASN B:90
BINDING SITE FOR RESIDUE NAG B 800
06
AC6
SOFTWARE
SER B:420 , ASN B:546
BINDING SITE FOR RESIDUE NAG B 801
07
AC7
SOFTWARE
ASP F:484 , ASN F:486
BINDING SITE FOR RESIDUE NAG F 1486
08
AC8
SOFTWARE
LYS D:68 , ASN F:510 , ASN F:512
BINDING SITE FOR RESIDUE NAG F 1512
09
AC9
SOFTWARE
LYS C:26 , ASN C:90
BINDING SITE FOR RESIDUE NAG C 800
10
BC1
SOFTWARE
SER C:420 , ASN C:546
BINDING SITE FOR RESIDUE NAG C 801
11
BC2
SOFTWARE
ASP G:484 , ASN G:486
BINDING SITE FOR RESIDUE NAG G 1486
12
BC3
SOFTWARE
LYS A:68 , ASN G:510 , ASN G:512
BINDING SITE FOR RESIDUE NAG G 1512
13
BC4
SOFTWARE
LYS D:26 , ASN D:90
BINDING SITE FOR RESIDUE NAG D 800
14
BC5
SOFTWARE
SER D:420 , ASN D:546
BINDING SITE FOR RESIDUE NAG D 801
15
BC6
SOFTWARE
LYS A:131 , ASP H:484 , ASN H:486
BINDING SITE FOR RESIDUE NAG H 1486
16
BC7
SOFTWARE
ASN H:510 , ASN H:512
BINDING SITE FOR RESIDUE NAG H 1512
[
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]
SAPs(SNPs)/Variants
(2, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_023082 (K26R, chain A/B/C/D, )
2: VAR_SPIKE_CVHNL_024 (H503R, chain E/F/G/H, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_023082
K
26
R
ACE2_HUMAN
Polymorphism
4646116
A/B/C/D
K
26
R
2
UniProt
VAR_SPIKE_CVHNL_024
*
H
503
R
SPIKE_CVHNL
---
---
E/F/G/H
H
503
R
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: ZINC_PROTEASE (A:371-380,B:371-380,C:371-380,D:37...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZINC_PROTEASE
PS00142
Neutral zinc metallopeptidases, zinc-binding region signature.
ACE2_HUMAN
371-380
4
A:371-380
B:371-380
C:371-380
D:371-380
[
close PROSITE info
]
Exons
(14, 56)
Info
All Exons
Exon 1.2 (A:19-62 (gaps) | B:19-62 (gaps) | ...)
Exon 1.3b (A:63-115 | B:63-115 | C:63-115 | D...)
Exon 1.4 (A:116-147 (gaps) | B:116-147 (gaps...)
Exon 1.5 (A:147-195 | B:147-195 | C:147-195 ...)
Exon 1.6 (A:195-232 | B:195-232 | C:195-232 ...)
Exon 1.7 (A:233-268 | B:233-268 | C:233-268 ...)
Exon 1.8 (A:268-300 | B:268-300 | C:268-300 ...)
Exon 1.9 (A:301-357 (gaps) | B:301-357 (gaps...)
Exon 1.10 (A:357-433 | B:357-433 | C:357-433 ...)
Exon 1.11 (A:433-481 | B:433-481 | C:433-481 ...)
Exon 1.12 (A:481-514 | B:481-514 | C:481-514 ...)
Exon 1.13 (A:514-555 | B:514-555 | C:514-555 ...)
Exon 1.14 (A:555-613 | B:555-613 | C:555-613 ...)
Exon 1.15 (A:613-614 | B:613-614 | C:613-614 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.2
02: Boundary 1.2/1.3b
03: Boundary 1.3b/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7
07: Boundary 1.7/1.8
08: Boundary 1.8/1.9
09: Boundary 1.9/1.10
10: Boundary 1.10/1.11
11: Boundary 1.11/1.12
12: Boundary 1.12/1.13
13: Boundary 1.13/1.14
14: Boundary 1.14/1.15
15: Boundary 1.15/1.16
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.2
ENST00000252519
2
ENSE00002198181
X:15619137-15618849
289
ACE2_HUMAN
1-62
62
4
A:19-62 (gaps)
B:19-62 (gaps)
C:19-62 (gaps)
D:19-62 (gaps)
44
44
44
44
1.3b
ENST00000252519
3b
ENSE00000894057
X:15613126-15612968
159
ACE2_HUMAN
63-115
53
4
A:63-115
B:63-115
C:63-115
D:63-115
53
53
53
53
1.4
ENST00000252519
4
ENSE00000894058
X:15610445-15610352
94
ACE2_HUMAN
116-147
32
4
A:116-147 (gaps)
B:116-147 (gaps)
C:116-147 (gaps)
D:116-147 (gaps)
32
32
32
32
1.5
ENST00000252519
5
ENSE00000894059
X:15609979-15609836
144
ACE2_HUMAN
147-195
49
4
A:147-195
B:147-195
C:147-195
D:147-195
49
49
49
49
1.6
ENST00000252519
6
ENSE00000894060
X:15607579-15607467
113
ACE2_HUMAN
195-232
38
4
A:195-232
B:195-232
C:195-232
D:195-232
38
38
38
38
1.7
ENST00000252519
7
ENSE00000894061
X:15605981-15605876
106
ACE2_HUMAN
233-268
36
4
A:233-268
B:233-268
C:233-268
D:233-268
36
36
36
36
1.8
ENST00000252519
8
ENSE00000894062
X:15603695-15603598
98
ACE2_HUMAN
268-300
33
4
A:268-300
B:268-300
C:268-300
D:268-300
33
33
33
33
1.9
ENST00000252519
9
ENSE00000894063
X:15599513-15599344
170
ACE2_HUMAN
301-357
57
4
A:301-357 (gaps)
B:301-357 (gaps)
C:301-357 (gaps)
D:301-357 (gaps)
57
57
57
57
1.10
ENST00000252519
10
ENSE00000894064
X:15596438-15596212
227
ACE2_HUMAN
357-433
77
4
A:357-433
B:357-433
C:357-433
D:357-433
77
77
77
77
1.11
ENST00000252519
11
ENSE00000894065
X:15593933-15593789
145
ACE2_HUMAN
433-481
49
4
A:433-481
B:433-481
C:433-481
D:433-481
49
49
49
49
1.12
ENST00000252519
12
ENSE00000894066
X:15591588-15591490
99
ACE2_HUMAN
481-514
34
4
A:481-514
B:481-514
C:481-514
D:481-514
34
34
34
34
1.13
ENST00000252519
13
ENSE00000894067
X:15590446-15590324
123
ACE2_HUMAN
514-555
42
4
A:514-555
B:514-555
C:514-555
D:514-555
42
42
42
42
1.14
ENST00000252519
14
ENSE00000894068
X:15589919-15589747
173
ACE2_HUMAN
555-613
59
4
A:555-613
B:555-613
C:555-613
D:555-613
59
59
59
59
1.15
ENST00000252519
15
ENSE00000894069
X:15588476-15588418
59
ACE2_HUMAN
613-632
20
4
A:613-614
B:613-614
C:613-614
D:613-614
2
2
2
2
1.16
ENST00000252519
16
ENSE00000894070
X:15585949-15585849
101
ACE2_HUMAN
633-666
34
0
-
-
1.17b
ENST00000252519
17b
ENSE00000894071
X:15584492-15584376
117
ACE2_HUMAN
666-705
40
0
-
-
1.18
ENST00000252519
18
ENSE00000894072
X:15582341-15582147
195
ACE2_HUMAN
705-770
66
0
-
-
1.19c
ENST00000252519
19c
ENSE00001334055
X:15580136-15579156
981
ACE2_HUMAN
770-805
36
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Peptidase_M2_3kbhD01 (D:19-613)
1b: PFAM_Peptidase_M2_3kbhD02 (D:19-613)
1c: PFAM_Peptidase_M2_3kbhD03 (D:19-613)
1d: PFAM_Peptidase_M2_3kbhD04 (D:19-613)
2a: PFAM_Corona_S1_3kbhH01 (H:482-602)
2b: PFAM_Corona_S1_3kbhH02 (H:482-602)
2c: PFAM_Corona_S1_3kbhH03 (H:482-602)
2d: PFAM_Corona_S1_3kbhH04 (H:482-602)
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Clans
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(
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(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MA
(251)
Family
:
Peptidase_M2
(20)
Homo sapiens (Human)
(10)
1a
Peptidase_M2-3kbhD01
D:19-613
1b
Peptidase_M2-3kbhD02
D:19-613
1c
Peptidase_M2-3kbhD03
D:19-613
1d
Peptidase_M2-3kbhD04
D:19-613
Clan
:
no clan defined [family: Corona_S1]
(1)
Family
:
Corona_S1
(1)
Human coronavirus NL63 (HCoV-NL63)
(1)
2a
Corona_S1-3kbhH01
H:482-602
2b
Corona_S1-3kbhH02
H:482-602
2c
Corona_S1-3kbhH03
H:482-602
2d
Corona_S1-3kbhH04
H:482-602
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