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1LVO
Asym. Unit
Info
Asym.Unit (312 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (105 KB)
Biol.Unit 3 (104 KB)
Biol.Unit 4 (305 KB)
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(1)
Title
:
STRUCTURE OF CORONAVIRUS MAIN PROTEINASE REVEALS COMBINATION OF A CHYMOTRYPSIN FOLD WITH AN EXTRA ALPHA-HELICAL DOMAIN
Authors
:
K. Anand, G. J. Palm, J. R. Mesters, S. G. Siddell, J. Ziebuhr, R. Hilgenfeld
Date
:
29 May 02 (Deposition) - 17 Jul 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.96
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: A,B,C,D,E,F (1x)
Keywords
:
3C Like, Corona, Proteinase, Chymotrypsin, Cysteine Histidine Dyad, Beta Barrel, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Anand, G. J. Palm, J. R. Mesters, S. G. Siddell, J. Ziebuhr, R. Hilgenfeld
Structure Of Coronavirus Main Proteinase Reveals Combination Of A Chymotrypsin Fold With An Extra Alpha-Helical Domain.
Embo J. V. 21 3213 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 42)
Info
All Hetero Components
1a: 1,4-DIETHYLENE DIOXIDE (DIOa)
1b: 1,4-DIETHYLENE DIOXIDE (DIOb)
1c: 1,4-DIETHYLENE DIOXIDE (DIOc)
1d: 1,4-DIETHYLENE DIOXIDE (DIOd)
1e: 1,4-DIETHYLENE DIOXIDE (DIOe)
1f: 1,4-DIETHYLENE DIOXIDE (DIOf)
1g: 1,4-DIETHYLENE DIOXIDE (DIOg)
1h: 1,4-DIETHYLENE DIOXIDE (DIOh)
1i: 1,4-DIETHYLENE DIOXIDE (DIOi)
2a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
2b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
2c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
2d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
2e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
2f: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDf)
3a: SULFATE ION (SO4a)
3aa: SULFATE ION (SO4aa)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
3y: SULFATE ION (SO4y)
3z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DIO
9
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
2
MRD
6
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
3
SO4
27
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(41, 41)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU C:179
BINDING SITE FOR RESIDUE SO4 C 3001
02
AC2
SOFTWARE
ARG C:130 , ASN C:196
BINDING SITE FOR RESIDUE SO4 C 3002
03
AC3
SOFTWARE
ASN A:168 , LEU A:192 , GLU A:193 , GLY A:194 , HOH A:4029
BINDING SITE FOR RESIDUE SO4 A 3003
04
AC4
SOFTWARE
ARG A:130 , LYS A:136 , ASN A:196 , HOH A:4135
BINDING SITE FOR RESIDUE SO4 A 3004
05
AC5
SOFTWARE
ASN C:168 , LEU C:192 , GLU C:193 , GLY C:194 , HOH C:4077
BINDING SITE FOR RESIDUE SO4 C 3005
06
AC6
SOFTWARE
ASN B:168 , GLU B:193 , GLY B:194 , HOH B:4075 , HOH B:4158
BINDING SITE FOR RESIDUE SO4 B 3006
07
AC7
SOFTWARE
HOH B:4178 , ASN E:168 , LEU E:192 , GLU E:193 , GLY E:194
BINDING SITE FOR RESIDUE SO4 E 3007
08
AC8
SOFTWARE
ARG D:130 , ASN D:196 , HOH D:4083
BINDING SITE FOR RESIDUE SO4 D 3008
09
AC9
SOFTWARE
ARG E:130 , HOH E:4100 , HOH E:4184 , HOH E:4210
BINDING SITE FOR RESIDUE SO4 E 3009
10
BC1
SOFTWARE
ASN F:168 , LEU F:192 , GLU F:193 , GLY F:194
BINDING SITE FOR RESIDUE SO4 F 3010
11
BC2
SOFTWARE
GLY A:214 , GLU A:215 , ARG A:216 , TRP A:217
BINDING SITE FOR RESIDUE SO4 A 3011
12
BC3
SOFTWARE
ASN D:168 , LEU D:192 , GLU D:193 , GLY D:194 , HOH D:4026
BINDING SITE FOR RESIDUE SO4 D 3012
13
BC4
SOFTWARE
ARG E:275 , THR E:276 , HOH E:4094
BINDING SITE FOR RESIDUE SO4 E 3013
14
BC5
SOFTWARE
ARG C:275 , THR C:276
BINDING SITE FOR RESIDUE SO4 C 3015
15
BC6
SOFTWARE
GLY D:214 , ARG D:216 , TRP D:217 , HOH D:4168
BINDING SITE FOR RESIDUE SO4 D 3016
16
BC7
SOFTWARE
ARG D:275 , THR D:276
BINDING SITE FOR RESIDUE SO4 D 3017
17
BC8
SOFTWARE
VAL E:60 , ARG E:61 , LEU E:62 , HIS E:63
BINDING SITE FOR RESIDUE SO4 E 3018
18
BC9
SOFTWARE
ARG F:216 , TRP F:217 , DIO F:2003
BINDING SITE FOR RESIDUE SO4 F 3019
19
CC1
SOFTWARE
LYS B:82 , PHE B:102 , PHE B:176
BINDING SITE FOR RESIDUE SO4 B 3020
20
CC2
SOFTWARE
ARG C:294 , ALA D:115 , SER D:123
BINDING SITE FOR RESIDUE SO4 D 3021
21
CC3
SOFTWARE
LYS A:103 , SER A:104
BINDING SITE FOR RESIDUE SO4 A 3022
22
CC4
SOFTWARE
GLY C:214 , GLU C:215 , ARG C:216 , TRP C:217 , ARG C:275 , HOH C:4035
BINDING SITE FOR RESIDUE SO4 C 3023
23
CC5
SOFTWARE
ARG F:61 , LEU F:62 , HIS F:63
BINDING SITE FOR RESIDUE SO4 F 3024
24
CC6
SOFTWARE
ARG F:130 , LYS F:136 , ASN F:196
BINDING SITE FOR RESIDUE SO4 F 3025
25
CC7
SOFTWARE
ARG B:19 , SER B:21 , HOH B:4070 , HOH B:4116
BINDING SITE FOR RESIDUE SO4 B 3026
26
CC8
SOFTWARE
ARG A:19 , SER A:21 , VAL A:26
BINDING SITE FOR RESIDUE SO4 A 3027
27
CC9
SOFTWARE
GLY B:273 , ARG E:216 , TRP E:217 , HOH E:4063 , HOH E:4132 , HOH E:4229 , HOH E:4230
BINDING SITE FOR RESIDUE DIO E 2001
28
DC1
SOFTWARE
SER E:123 , HOH E:4185 , MET F:6
BINDING SITE FOR RESIDUE DIO E 2002
29
DC2
SOFTWARE
GLY F:274 , ARG F:275 , THR F:276 , SO4 F:3019
BINDING SITE FOR RESIDUE DIO F 2003
30
DC3
SOFTWARE
ASN A:112 , GLU A:291
BINDING SITE FOR RESIDUE DIO A 2004
31
DC4
SOFTWARE
SER A:131 , GLN A:132 , GLY A:133
BINDING SITE FOR RESIDUE DIO A 2005
32
DC5
SOFTWARE
GLY A:122 , SER A:123 , HOH A:4112
BINDING SITE FOR RESIDUE DIO A 2006
33
DC6
SOFTWARE
PHE B:139 , CYS B:144 , HIS B:162 , GLU B:165
BINDING SITE FOR RESIDUE DIO B 2007
34
DC7
SOFTWARE
SER C:223 , MET C:224 , SER C:225 , SER C:228
BINDING SITE FOR RESIDUE DIO C 2008
35
DC8
SOFTWARE
LYS C:136 , HOH C:4124 , GLY D:2 , ASN D:213
BINDING SITE FOR RESIDUE DIO C 2009
36
DC9
SOFTWARE
HIS A:41 , HIS A:163 , LEU A:164 , GLN A:187 , PRO A:188
BINDING SITE FOR RESIDUE MRD A 4001
37
EC1
SOFTWARE
HIS B:41 , THR B:47 , ILE B:51 , TYR B:53 , LEU B:164 , ASP B:186 , HOH B:4192
BINDING SITE FOR RESIDUE MRD B 4002
38
EC2
SOFTWARE
HIS C:41 , THR C:47 , ILE C:51 , TYR C:53 , LEU C:164 , ASP C:186
BINDING SITE FOR RESIDUE MRD C 4003
39
EC3
SOFTWARE
HIS D:41 , ILE D:51 , TYR D:53 , LEU D:164 , ASP D:186 , GLN D:187 , PRO D:188
BINDING SITE FOR RESIDUE MRD D 4004
40
EC4
SOFTWARE
HIS E:41 , THR E:47 , HIS E:163 , LEU E:164 , ASP E:186 , GLN E:187 , HOH E:4045
BINDING SITE FOR RESIDUE MRD E 4005
41
EC5
SOFTWARE
HIS F:41 , THR F:47 , ASP F:186 , GLN F:187 , PRO F:188
BINDING SITE FOR RESIDUE MRD F 4006
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: M_PRO (A:1-299,B:1-300,C:1-300,D:1-301,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
M_PRO
PS51442
Coronavirus main protease (M-pro) domain profile.
R1AB_CVPPU
2879-3180
6
A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299
R1A_CVPPU
2879-3180
6
A:1-299
B:1-300
C:1-300
D:1-301
E:1-299
F:1-299
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1lvoa_ (A:)
1b: SCOP_d1lvob_ (B:)
1c: SCOP_d1lvoc_ (C:)
1d: SCOP_d1lvod_ (D:)
1e: SCOP_d1lvoe_ (E:)
1f: SCOP_d1lvof_ (F:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Viral cysteine protease of trypsin fold
(145)
Protein domain
:
Coronavirus main proteinase (3Cl-pro, putative coronavirus nsp2)
(75)
Transmissible gastroenteritis virus [TaxId: 11149]
(3)
1a
d1lvoa_
A:
1b
d1lvob_
B:
1c
d1lvoc_
C:
1d
d1lvod_
D:
1e
d1lvoe_
E:
1f
d1lvof_
F:
[
close SCOP info
]
CATH Domains
(2, 18)
Info
all CATH domains
1a: CATH_1lvoA03 (A:197-299)
1b: CATH_1lvoB03 (B:197-299)
1c: CATH_1lvoC03 (C:197-299)
1d: CATH_1lvoD03 (D:197-299)
1e: CATH_1lvoE03 (E:197-299)
1f: CATH_1lvoF03 (F:197-299)
2a: CATH_1lvoA01 (A:14-97)
2b: CATH_1lvoB01 (B:14-97)
2c: CATH_1lvoA02 (A:98-185)
2d: CATH_1lvoB02 (B:98-185)
2e: CATH_1lvoC02 (C:98-185)
2f: CATH_1lvoD02 (D:98-185)
2g: CATH_1lvoE02 (E:98-185)
2h: CATH_1lvoF02 (F:98-185)
2i: CATH_1lvoC01 (C:14-97)
2j: CATH_1lvoD01 (D:14-97)
2k: CATH_1lvoE01 (E:14-97)
2l: CATH_1lvoF01 (F:14-97)
View:
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Architectures
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
main proteinase (3clpro) structure, domain 3
(38)
Homologous Superfamily
:
main proteinase (3clpro) structure, domain 3
(38)
Transmissible gastroenteritis virus. Organism_taxid: 11149.
(2)
1a
1lvoA03
A:197-299
1b
1lvoB03
B:197-299
1c
1lvoC03
C:197-299
1d
1lvoD03
D:197-299
1e
1lvoE03
E:197-299
1f
1lvoF03
F:197-299
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Transmissible gastroenteritis virus. Organism_taxid: 11149.
(2)
2a
1lvoA01
A:14-97
2b
1lvoB01
B:14-97
2c
1lvoA02
A:98-185
2d
1lvoB02
B:98-185
2e
1lvoC02
C:98-185
2f
1lvoD02
D:98-185
2g
1lvoE02
E:98-185
2h
1lvoF02
F:98-185
2i
1lvoC01
C:14-97
2j
1lvoD01
D:14-97
2k
1lvoE01
E:14-97
2l
1lvoF01
F:14-97
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Peptidase_C30_1lvoF01 (F:29-299)
1b: PFAM_Peptidase_C30_1lvoF02 (F:29-299)
1c: PFAM_Peptidase_C30_1lvoF03 (F:29-299)
1d: PFAM_Peptidase_C30_1lvoF04 (F:29-299)
1e: PFAM_Peptidase_C30_1lvoF05 (F:29-299)
1f: PFAM_Peptidase_C30_1lvoF06 (F:29-299)
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Clans
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Families
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Organisms
(
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(
)
Clan
:
Peptidase_PA
(797)
Family
:
Peptidase_C30
(30)
Porcine transmissible gastroenteritis coronavirus (strain Purdue) (TGEV)
(1)
1a
Peptidase_C30-1lvoF01
F:29-299
1b
Peptidase_C30-1lvoF02
F:29-299
1c
Peptidase_C30-1lvoF03
F:29-299
1d
Peptidase_C30-1lvoF04
F:29-299
1e
Peptidase_C30-1lvoF05
F:29-299
1f
Peptidase_C30-1lvoF06
F:29-299
[
close Pfam info
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