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3CDW
Asym. Unit
Info
Asym.Unit (98 KB)
Biol.Unit 1 (91 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3 RNA-DEPENDENT RNA POLYMERASE (3DPOL) IN COMPLEX WITH PROTEIN PRIMER VPG AND A PYROPHOSPHATE
Authors
:
A. Gruez, B. Selisko, M. Roberts, G. Bricogne, C. Bussetta, B. Canard
Date
:
27 Feb 08 (Deposition) - 22 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,H
Biol. Unit 1: A,H (1x)
Keywords
:
Coxsackievirus, Rna-Dependent Rna Polymerase, Protein Primer, Vpg, Vizier Viral Enzymes Involved In Replication, Transferase-Viral Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Gruez, B. Selisko, M. Roberts, G. Bricogne, C. Bussetta, I. Jabafi, B. Coutard, A. M. De Palma, J. Neyts, B. Canard
The Crystal Structure Of Coxsackievirus B3 Rna-Dependent Rn Polymerase In Complex With Its Protein Primer Vpg Confirms The Existence Of A Second Vpg Binding Site On Picornavirida Polymerases
J. Virol. V. 82 9577 2008
[
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Hetero Components
(4, 41)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
3a: GLYCEROL (GOLa)
3aa: GLYCEROL (GOLaa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
3w: GLYCEROL (GOLw)
3x: GLYCEROL (GOLx)
3y: GLYCEROL (GOLy)
3z: GLYCEROL (GOLz)
4a: PYROPHOSPHATE 2- (POPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
CL
7
Ligand/Ion
CHLORIDE ION
3
GOL
27
Ligand/Ion
GLYCEROL
4
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
[
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Sites
(39, 39)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:314 , LYS A:315 , GLY A:316
BINDING SITE FOR RESIDUE CL A 469
02
AC2
SOFTWARE
LYS A:220 , HIS A:466 , HIS A:468
BINDING SITE FOR RESIDUE CL A 470
03
AC3
SOFTWARE
GLU A:35 , HIS A:399 , LYS A:436
BINDING SITE FOR RESIDUE CL A 471
04
AC4
SOFTWARE
CYS A:212 , ASP A:213
BINDING SITE FOR RESIDUE CL A 472
05
AC5
SOFTWARE
ARG A:163 , LYS A:167 , ARG A:174
BINDING SITE FOR RESIDUE CL A 475
06
AC6
SOFTWARE
PRO A:20 , SER A:21 , LYS A:22
BINDING SITE FOR RESIDUE ACT A 476
07
AC7
SOFTWARE
LYS A:22 , ARG A:44
BINDING SITE FOR RESIDUE ACT A 477
08
AC8
SOFTWARE
ASN A:425 , GLY A:426 , GLU A:427 , HIS A:428 , GLU A:429
BINDING SITE FOR RESIDUE ACT A 478
09
AC9
SOFTWARE
SER A:132 , LYS A:133 , LYS A:134
BINDING SITE FOR RESIDUE ACT A 479
10
BC1
SOFTWARE
THR A:68 , ALA A:247
BINDING SITE FOR RESIDUE ACT A 480
11
BC2
SOFTWARE
HIS A:69
BINDING SITE FOR RESIDUE ACT A 481
12
BC3
SOFTWARE
LYS A:38 , LEU A:162 , ARG A:163 , SER A:164 , LYS A:167 , ARG A:174 , LYS A:376
BINDING SITE FOR RESIDUE POP A 482
13
BC4
SOFTWARE
HIS A:199 , SER A:295 , TYR A:327
BINDING SITE FOR RESIDUE GOL A 483
14
BC5
SOFTWARE
GLY A:290 , CYS A:291 , THR A:294 , SER A:295
BINDING SITE FOR RESIDUE GOL A 484
15
BC6
SOFTWARE
LYS A:38 , ASP A:397 , SER A:401
BINDING SITE FOR RESIDUE GOL A 485
16
BC7
SOFTWARE
GLN A:384 , TYR A:385 , ARG A:455 , LEU A:459
BINDING SITE FOR RESIDUE GOL A 486
17
BC8
SOFTWARE
SER A:452 , THR A:453 , ARG A:456
BINDING SITE FOR RESIDUE GOL A 487
18
BC9
SOFTWARE
ARG A:416 , PRO A:449 , ALA A:450 , THR A:453
BINDING SITE FOR RESIDUE GOL A 488
19
CC1
SOFTWARE
CYS A:212 , TYR A:327
BINDING SITE FOR RESIDUE GOL A 489
20
CC2
SOFTWARE
ASP A:397
BINDING SITE FOR RESIDUE GOL A 490
21
CC3
SOFTWARE
THR A:370 , TYR A:378 , ARG A:380 , PRO H:14
BINDING SITE FOR RESIDUE GOL A 491
22
CC4
SOFTWARE
ASN A:151 , LYS A:261 , ASN A:264
BINDING SITE FOR RESIDUE GOL A 492
23
CC5
SOFTWARE
PHE A:246 , ALA A:247 , ILE A:266 , ASP A:267 , CYS A:270 , ASN A:271
BINDING SITE FOR RESIDUE GOL A 493
24
CC6
SOFTWARE
ILE A:3 , ILE A:6 , GLU A:55 , LYS A:279 , TYR A:281
BINDING SITE FOR RESIDUE GOL A 494
25
CC7
SOFTWARE
LEU A:43 , ARG A:44 , SER A:45 , GLU A:55 , TYR A:276 , ARG A:277
BINDING SITE FOR RESIDUE GOL A 495
26
CC8
SOFTWARE
PHE A:232 , ASP A:233 , ASP A:330 , ASP A:359 , THR A:373 , PHE A:374
BINDING SITE FOR RESIDUE GOL A 496
27
CC9
SOFTWARE
ILE A:58 , PHE A:59 , LYS A:61 , TYR A:62 , ALA A:239
BINDING SITE FOR RESIDUE GOL A 497
28
DC1
SOFTWARE
LYS A:61 , ARG A:174 , GLY A:236
BINDING SITE FOR RESIDUE GOL A 498
29
DC2
SOFTWARE
LYS A:10 , GLY A:316 , ASP A:318 , TYR A:335 , TRP A:337
BINDING SITE FOR RESIDUE GOL A 499
30
DC3
SOFTWARE
LEU A:107 , ARG A:188 , TYR A:195 , HIS A:199 , SER A:292 , GLY A:293
BINDING SITE FOR RESIDUE GOL A 500
31
DC4
SOFTWARE
HIS A:31 , GLY A:36 , ARG A:403 , TRP A:404
BINDING SITE FOR RESIDUE GOL A 501
32
DC5
SOFTWARE
ALA A:381 , ASP A:382 , GLU A:383 , HIS A:390 , LYS H:10
BINDING SITE FOR RESIDUE GOL A 502
33
DC6
SOFTWARE
GLY A:426 , GLU A:427 , HIS A:428 , PHE A:451
BINDING SITE FOR RESIDUE GOL A 503
34
DC7
SOFTWARE
ALA A:12 , GLY A:13 , ILE A:339
BINDING SITE FOR RESIDUE GOL A 504
35
DC8
SOFTWARE
LYS A:140 , LYS A:147 , GLU A:346 , LYS A:349
BINDING SITE FOR RESIDUE GOL A 505
36
DC9
SOFTWARE
THR A:114 , SER A:115
BINDING SITE FOR RESIDUE GOL A 506
37
EC1
SOFTWARE
ASP A:47 , PRO A:48 , ARG A:49
BINDING SITE FOR RESIDUE GOL A 507
38
EC2
SOFTWARE
GLU A:39 , PRO A:40 , TRP A:404
BINDING SITE FOR RESIDUE GOL A 508
39
EC3
SOFTWARE
PRO A:386 , THR A:447 , PRO H:7
BINDING SITE FOR RESIDUE GOL A 509
[
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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, 1)
Info
All PROSITE Patterns/Profiles
1: RDRP_SSRNA_POS (A:227-343)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RDRP_SSRNA_POS
PS50507
RdRp of positive ssRNA viruses catalytic domain profile.
POLG_CXB3N
1950-2066
1
A:227-343
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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, 1)
Info
All SCOP Domains
1a: SCOP_d3cdwa_ (A:)
View:
Select:
Label:
Classes
(
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(
)
Folds
(
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(
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Superfamilies
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(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
RNA-dependent RNA-polymerase
(253)
Protein domain
:
automated matches
(100)
Coxsackievirus b3 [TaxId: 103903]
(2)
1a
d3cdwa_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
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Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain H
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