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1LVO
Biol. Unit 4
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, 15)
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
4
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
2
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
3
SO4
9
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 only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 12)
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
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
(no "Exon" information available for biological units yet)
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:
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Classes
(
)
(
)
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(
)
(
)
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(
)
(
)
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)
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Topologies
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(
)
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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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
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