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3PKP
Asym. Unit
Info
Asym.Unit (787 KB)
Biol.Unit 1 (392 KB)
Biol.Unit 2 (395 KB)
Biol.Unit 3 (201 KB)
Biol.Unit 4 (200 KB)
Biol.Unit 5 (202 KB)
Biol.Unit 6 (201 KB)
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(1)
Title
:
Q83S VARIANT OF S. ENTERICA RMLA WITH DATP
Authors
:
A. Chang, R. Moretti, C. A. Bingman, J. S. Thorson, G. N. Phillips Jr. , C Eukaryotic Structural Genomics (Cesg)
Date
:
11 Nov 10 (Deposition) - 12 Jan 11 (Release) - 27 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,I,J,K,L
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: I,J,K,L (1x)
Biol. Unit 3: A,B (1x)
Biol. Unit 4: C,D (1x)
Biol. Unit 5: I,J (1x)
Biol. Unit 6: K,L (1x)
Keywords
:
Nucleotidylyltransferase, Directed Evolution, Structural Genomics, Psi-2, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Moretti, A. Chang, P. Peltier-Pain, C. A. Bingman, G. N. Phillips, J. S. Thorson
Expanding The Nucleotide And Sugar 1-Phosphate Promiscuity Of Nucleotidyltransferase Rmla Via Directed Evolution.
J. Biol. Chem. V. 286 13235 2011
[
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPa)
1b: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPb)
1c: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPc)
1d: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPd)
1e: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPe)
1f: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPf)
1g: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPg)
1h: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE (DTPh)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
2g: MAGNESIUM ION (MGg)
2h: MAGNESIUM ION (MGh)
2i: MAGNESIUM ION (MGi)
2j: MAGNESIUM ION (MGj)
2k: MAGNESIUM ION (MGk)
2l: MAGNESIUM ION (MGl)
2m: MAGNESIUM ION (MGm)
2n: MAGNESIUM ION (MGn)
2o: MAGNESIUM ION (MGo)
2p: MAGNESIUM ION (MGp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTP
8
Ligand/Ion
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2
MG
16
Ligand/Ion
MAGNESIUM ION
[
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:9 , ALA A:10 , GLY A:11 , GLY A:12 , SER A:13 , GLY A:14 , THR A:15 , ARG A:16 , LYS A:26 , GLN A:27 , SER A:83 , SER A:85 , PRO A:86 , GLY A:110 , ASP A:111 , MG A:501 , MG A:502
BINDING SITE FOR RESIDUE DTP A 500
02
AC2
SOFTWARE
ARG A:16 , ASP A:111 , ASP A:226 , DTP A:500
BINDING SITE FOR RESIDUE MG A 501
03
AC3
SOFTWARE
DTP A:500
BINDING SITE FOR RESIDUE MG A 502
04
AC4
SOFTWARE
LEU B:9 , GLY B:11 , GLY B:12 , SER B:13 , GLY B:14 , THR B:15 , ARG B:16 , LYS B:26 , GLN B:27 , SER B:83 , SER B:85 , PRO B:86 , GLY B:110 , ASP B:111 , MG B:501 , MG B:502
BINDING SITE FOR RESIDUE DTP B 500
05
AC5
SOFTWARE
ARG B:16 , ASP B:111 , ASP B:226 , DTP B:500
BINDING SITE FOR RESIDUE MG B 501
06
AC6
SOFTWARE
DTP B:500
BINDING SITE FOR RESIDUE MG B 502
07
AC7
SOFTWARE
LEU C:9 , GLY C:11 , GLY C:12 , SER C:13 , GLY C:14 , THR C:15 , ARG C:16 , LYS C:26 , GLN C:27 , SER C:83 , SER C:85 , PRO C:86 , GLY C:110 , ASP C:111 , MG C:501 , MG C:502 , LYS D:278
BINDING SITE FOR RESIDUE DTP C 500
08
AC8
SOFTWARE
ARG C:16 , ASP C:111 , ASP C:226 , DTP C:500
BINDING SITE FOR RESIDUE MG C 501
09
AC9
SOFTWARE
DTP C:500
BINDING SITE FOR RESIDUE MG C 502
10
BC1
SOFTWARE
LEU D:9 , GLY D:11 , GLY D:12 , SER D:13 , GLY D:14 , THR D:15 , ARG D:16 , LYS D:26 , GLN D:27 , SER D:83 , SER D:85 , PRO D:86 , GLY D:110 , ASP D:111 , MG D:501 , MG D:502
BINDING SITE FOR RESIDUE DTP D 500
11
BC2
SOFTWARE
ASP D:111 , ASP D:226 , DTP D:500
BINDING SITE FOR RESIDUE MG D 501
12
BC3
SOFTWARE
DTP D:500
BINDING SITE FOR RESIDUE MG D 502
13
BC4
SOFTWARE
LEU I:9 , GLY I:11 , GLY I:12 , SER I:13 , GLY I:14 , THR I:15 , ARG I:16 , LYS I:26 , GLN I:27 , SER I:83 , SER I:85 , PRO I:86 , GLY I:110 , ASP I:111 , MG I:501 , MG I:502 , HOH J:313
BINDING SITE FOR RESIDUE DTP I 500
14
BC5
SOFTWARE
ASP I:111 , ASP I:226 , HOH I:313 , DTP I:500
BINDING SITE FOR RESIDUE MG I 501
15
BC6
SOFTWARE
DTP I:500
BINDING SITE FOR RESIDUE MG I 502
16
BC7
SOFTWARE
LEU J:9 , ALA J:10 , GLY J:11 , GLY J:12 , SER J:13 , GLY J:14 , THR J:15 , ARG J:16 , LYS J:26 , GLN J:27 , SER J:83 , SER J:85 , PRO J:86 , GLY J:110 , ASP J:111 , HOH J:304 , MG J:501 , MG J:502
BINDING SITE FOR RESIDUE DTP J 500
17
BC8
SOFTWARE
ASP J:111 , ASP J:226 , DTP J:500
BINDING SITE FOR RESIDUE MG J 501
18
BC9
SOFTWARE
DTP J:500
BINDING SITE FOR RESIDUE MG J 502
19
CC1
SOFTWARE
GLY K:11 , GLY K:12 , SER K:13 , GLY K:14 , THR K:15 , ARG K:16 , LYS K:26 , GLN K:27 , SER K:83 , SER K:85 , PRO K:86 , GLY K:110 , ASP K:111 , MG K:501 , MG K:502
BINDING SITE FOR RESIDUE DTP K 500
20
CC2
SOFTWARE
ARG K:16 , ASP K:111 , ASP K:226 , DTP K:500
BINDING SITE FOR RESIDUE MG K 501
21
CC3
SOFTWARE
DTP K:500
BINDING SITE FOR RESIDUE MG K 502
22
CC4
SOFTWARE
LEU L:9 , GLY L:11 , GLY L:12 , SER L:13 , GLY L:14 , THR L:15 , ARG L:16 , LYS L:26 , GLN L:27 , SER L:83 , SER L:85 , PRO L:86 , GLY L:110 , ASP L:111 , MG L:501 , MG L:502
BINDING SITE FOR RESIDUE DTP L 500
23
CC5
SOFTWARE
ARG L:16 , ASP L:111 , ASP L:226 , DTP L:500
BINDING SITE FOR RESIDUE MG L 501
24
CC6
SOFTWARE
DTP L:500
BINDING SITE FOR RESIDUE MG L 502
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3pkpa_ (A:)
1b: SCOP_d3pkpk_ (K:)
1c: SCOP_d3pkpl_ (L:)
1d: SCOP_d3pkpb_ (B:)
1e: SCOP_d3pkpc_ (C:)
1f: SCOP_d3pkpd_ (D:)
1g: SCOP_d3pkpi_ (I:)
1h: SCOP_d3pkpj_ (J:)
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
glucose-1-phosphate thymidylyltransferase
(43)
Protein domain
:
automated matches
(12)
Salmonella typhimurium [TaxId: 90371]
(2)
1a
d3pkpa_
A:
1b
d3pkpk_
K:
1c
d3pkpl_
L:
1d
d3pkpb_
B:
1e
d3pkpc_
C:
1f
d3pkpd_
D:
1g
d3pkpi_
I:
1h
d3pkpj_
J:
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_NTP_transferase_3pkpL01 (L:5-243)
1b: PFAM_NTP_transferase_3pkpL02 (L:5-243)
1c: PFAM_NTP_transferase_3pkpL03 (L:5-243)
1d: PFAM_NTP_transferase_3pkpL04 (L:5-243)
1e: PFAM_NTP_transferase_3pkpL05 (L:5-243)
1f: PFAM_NTP_transferase_3pkpL06 (L:5-243)
1g: PFAM_NTP_transferase_3pkpL07 (L:5-243)
1h: PFAM_NTP_transferase_3pkpL08 (L:5-243)
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Clans
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)
(
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(
)
Organisms
(
)
(
)
Clan
:
GT-A
(172)
Family
:
NTP_transferase
(15)
Salmonella typhimurium
(2)
1a
NTP_transferase-3pkpL01
L:5-243
1b
NTP_transferase-3pkpL02
L:5-243
1c
NTP_transferase-3pkpL03
L:5-243
1d
NTP_transferase-3pkpL04
L:5-243
1e
NTP_transferase-3pkpL05
L:5-243
1f
NTP_transferase-3pkpL06
L:5-243
1g
NTP_transferase-3pkpL07
L:5-243
1h
NTP_transferase-3pkpL08
L:5-243
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