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1LVO
Biol. Unit 3
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
)
[
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Hetero Components
(3, 13)
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
3
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
2
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
3
SO4
8
Ligand/Ion
SULFATE ION
[
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Sites
(13, 13)
Info
All Sites
01: AC7 (SOFTWARE)
02: AC9 (SOFTWARE)
03: BC1 (SOFTWARE)
04: BC4 (SOFTWARE)
05: BC8 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC5 (SOFTWARE)
08: CC6 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
12: EC4 (SOFTWARE)
13: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC7
SOFTWARE
HOH B:4178 , ASN E:168 , LEU E:192 , GLU E:193 , GLY E:194
BINDING SITE FOR RESIDUE SO4 E 3007
02
AC9
SOFTWARE
ARG E:130 , HOH E:4100 , HOH E:4184 , HOH E:4210
BINDING SITE FOR RESIDUE SO4 E 3009
03
BC1
SOFTWARE
ASN F:168 , LEU F:192 , GLU F:193 , GLY F:194
BINDING SITE FOR RESIDUE SO4 F 3010
04
BC4
SOFTWARE
ARG E:275 , THR E:276 , HOH E:4094
BINDING SITE FOR RESIDUE SO4 E 3013
05
BC8
SOFTWARE
VAL E:60 , ARG E:61 , LEU E:62 , HIS E:63
BINDING SITE FOR RESIDUE SO4 E 3018
06
BC9
SOFTWARE
ARG F:216 , TRP F:217 , DIO F:2003
BINDING SITE FOR RESIDUE SO4 F 3019
07
CC5
SOFTWARE
ARG F:61 , LEU F:62 , HIS F:63
BINDING SITE FOR RESIDUE SO4 F 3024
08
CC6
SOFTWARE
ARG F:130 , LYS F:136 , ASN F:196
BINDING SITE FOR RESIDUE SO4 F 3025
09
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
10
DC1
SOFTWARE
SER E:123 , HOH E:4185 , MET F:6
BINDING SITE FOR RESIDUE DIO E 2002
11
DC2
SOFTWARE
GLY F:274 , ARG F:275 , THR F:276 , SO4 F:3019
BINDING SITE FOR RESIDUE DIO F 2003
12
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
13
EC5
SOFTWARE
HIS F:41 , THR F:47 , ASP F:186 , GLN F:187 , PRO F:188
BINDING SITE FOR RESIDUE MRD F 4006
[
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]
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, 4)
Info
All PROSITE Patterns/Profiles
1: M_PRO (E:1-299,F:1-299)
;
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
2
-
-
-
-
E:1-299
F:1-299
R1A_CVPPU
2879-3180
2
-
-
-
-
E:1-299
F:1-299
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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(
)
(
)
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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)
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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)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
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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Asym.Unit (312 KB)
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