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1G1L
Biol. Unit 1
Info
Asym.Unit (903 KB)
Biol.Unit 1 (452 KB)
Biol.Unit 2 (449 KB)
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(1)
Title
:
THE STRUCTURAL BASIS OF THE CATALYTIC MECHANISM AND REGULATION OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE (RMLA). TDP-GLUCOSE COMPLEX.
Authors
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naimsmith
Date
:
12 Oct 00 (Deposition) - 27 Dec 00 (Release) - 23 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
L-Rhamnose, Nucleotidyltransferase, Pyrophosphorylase, Thymidylyltransferase, Allostery, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. Blankenfeldt, M. Asuncion, J. S. Lam, J. H. Naismith
The Structural Basis Of The Catalytic Mechanism And Regulation Of Glucose-1-Phosphate Thymidylyltransferase (Rmla).
Embo J. V. 19 6652 2000
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(3, 21)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
2a: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUa)
2b: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUb)
2c: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUc)
2d: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUd)
2e: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUe)
2f: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUf)
2g: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUg)
2h: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUh)
2i: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUi)
2j: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUj)
2k: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUk)
2l: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUl)
2m: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUm)
2n: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUn)
2o: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUo)
2p: 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALP... (DAUp)
3a: SULFATE ION (SO4a)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
2
Ligand/Ion
CITRIC ACID
2
DAU
8
Ligand/Ion
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
3
SO4
11
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC6 (SOFTWARE)
16: CC7 (SOFTWARE)
17: CC8 (SOFTWARE)
18: CC9 (SOFTWARE)
19: DC1 (SOFTWARE)
20: DC2 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC4 (SOFTWARE)
23: EC4 (SOFTWARE)
24: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:12 , GLY A:13 , THR A:14 , ARG A:15 , LYS A:25 , HOH A:4062
BINDING SITE FOR RESIDUE SO4 A 3700
02
AC2
SOFTWARE
SER B:12 , GLY B:13 , THR B:14 , ARG B:15 , LYS B:25 , HOH B:3986 , HOH B:4080 , HOH B:4153 , HOH B:4203 , HOH B:4205
BINDING SITE FOR RESIDUE SO4 B 3701
03
AC5
SOFTWARE
ARG A:62 , HOH A:3985 , ARG B:62 , HOH C:4051
BINDING SITE FOR RESIDUE SO4 A 3802
04
AC6
SOFTWARE
ARG A:128 , GLU A:215 , HOH A:4030 , HOH A:4084 , ASP F:151 , GLN F:152 , HOH F:4059
BINDING SITE FOR RESIDUE SO4 A 3803
05
AC7
SOFTWARE
GLU B:160 , GLU B:161 , ARG B:194 , ARG B:204 , HOH B:3899 , HOH B:3925 , HOH B:4108
BINDING SITE FOR RESIDUE SO4 B 3804
06
AC8
SOFTWARE
HOH B:4118 , ARG C:62 , HOH C:3935 , HOH C:4021 , ARG D:62 , HOH D:3955
BINDING SITE FOR RESIDUE SO4 C 3805
07
AC9
SOFTWARE
GLN C:127 , ARG C:128 , GLN C:129 , THR C:130
BINDING SITE FOR RESIDUE SO4 C 3806
08
BC1
SOFTWARE
GLN D:127 , ARG D:128 , GLN D:129 , THR D:130
BINDING SITE FOR RESIDUE SO4 D 3807
09
BC4
SOFTWARE
ARG B:128 , GLU B:215 , ASP E:151 , GLN E:152 , HOH E:3989 , HOH E:3990
BINDING SITE FOR RESIDUE SO4 E 3810
10
BC6
SOFTWARE
ASP C:151 , GLN C:152 , HOH C:4014 , HOH C:4093 , ARG G:128 , GLU G:215 , HOH G:3951 , HOH G:4101
BINDING SITE FOR RESIDUE SO4 G 3812
11
BC9
SOFTWARE
ASP D:151 , GLN D:152 , HOH D:3943 , HOH D:3949 , HOH D:4074 , ARG H:128 , GLU H:215 , HOH H:3892
BINDING SITE FOR RESIDUE SO4 H 3815
12
CC2
SOFTWARE
GLU A:160 , GLU A:161 , ARG A:194 , ARG A:204 , HOH A:3908 , HOH A:3914 , HOH A:3992 , HOH A:4201 , HOH B:4183
BINDING SITE FOR RESIDUE SO4 A 3817
13
CC3
SOFTWARE
HIS A:116 , DAU A:3501 , HOH A:3829 , HOH A:3921 , HOH A:3927 , HOH A:3997 , LEU C:121 , TYR C:221 , HOH C:3905
BINDING SITE FOR RESIDUE SO4 A 3818
14
CC4
SOFTWARE
LEU B:121 , TYR B:221 , HOH B:3816 , HIS D:116 , DAU D:3507 , HOH D:3892 , HOH D:3933
BINDING SITE FOR RESIDUE SO4 D 3819
15
CC6
SOFTWARE
LEU A:8 , GLY A:10 , GLY A:11 , GLN A:26 , GLN A:82 , PRO A:85 , ASP A:86 , GLY A:87 , LEU A:88 , LEU A:108 , GLY A:109 , ASP A:110 , ASN A:111 , TYR A:145 , GLY A:146 , GLU A:161 , LYS A:162 , VAL A:172 , GLU A:196 , THR A:200 , HOH A:3819 , HOH A:3904 , HOH A:4168 , HOH A:4203 , HOH A:4224
BINDING SITE FOR RESIDUE DAU A 3500
16
CC7
SOFTWARE
LEU A:45 , TYR A:114 , GLY A:115 , HIS A:116 , ASP A:117 , PHE A:118 , HIS A:119 , GLU A:120 , VAL A:250 , ALA A:251 , GLU A:255 , ILE A:256 , ARG A:259 , TYR A:293 , SO4 A:3818 , HOH A:3839 , HOH A:3847 , HOH A:3850 , HOH A:3862 , HOH A:3900 , HOH A:3927 , HOH A:4023 , HOH A:4049 , HOH A:4184 , ILE C:216 , GLY C:218 , ARG C:219 , GLY C:220
BINDING SITE FOR RESIDUE DAU A 3501
17
CC8
SOFTWARE
LEU B:8 , GLY B:10 , GLY B:11 , ARG B:15 , GLN B:26 , GLN B:82 , PRO B:85 , ASP B:86 , GLY B:87 , LEU B:88 , LEU B:108 , GLY B:109 , ASP B:110 , ASN B:111 , TYR B:145 , GLY B:146 , GLU B:161 , LYS B:162 , VAL B:172 , THR B:200 , HOH B:3832 , HOH B:3856 , HOH B:3915 , HOH B:3969 , HOH B:4199 , HOH B:4200 , HOH B:4201
BINDING SITE FOR RESIDUE DAU B 3502
18
CC9
SOFTWARE
LEU B:45 , TYR B:114 , GLY B:115 , HIS B:116 , ASP B:117 , PHE B:118 , HIS B:119 , GLU B:120 , VAL B:250 , ALA B:251 , GLU B:255 , ILE B:256 , TYR B:293 , HOH B:3817 , HOH B:3826 , HOH B:3835 , HOH B:3863 , HOH B:3876 , HOH B:3887 , HOH B:3971 , HOH B:4112 , ILE D:216 , GLY D:218 , ARG D:219 , GLY D:220
BINDING SITE FOR RESIDUE DAU B 3503
19
DC1
SOFTWARE
LEU C:8 , GLY C:10 , GLY C:11 , LYS C:25 , GLN C:26 , GLN C:82 , PRO C:85 , ASP C:86 , GLY C:87 , LEU C:88 , LEU C:108 , GLY C:109 , ASP C:110 , ASN C:111 , TYR C:145 , GLY C:146 , GLU C:161 , LYS C:162 , VAL C:172 , THR C:200 , HOH C:3814 , HOH C:3852 , HOH C:3977 , HOH C:4121 , HOH C:4146 , HOH C:4147 , HOH C:4149 , HOH C:4154
BINDING SITE FOR RESIDUE DAU C 3504
20
DC2
SOFTWARE
ILE A:216 , GLY A:218 , ARG A:219 , GLY A:220 , LEU C:45 , TYR C:114 , GLY C:115 , HIS C:116 , ASP C:117 , PHE C:118 , HIS C:119 , GLU C:120 , VAL C:250 , ALA C:251 , GLU C:255 , ILE C:256 , ARG C:259 , TYR C:293 , HOH C:3810 , HOH C:3826 , HOH C:3832 , HOH C:3850 , HOH C:3880 , HOH C:3979
BINDING SITE FOR RESIDUE DAU C 3505
21
DC3
SOFTWARE
LEU D:8 , GLY D:10 , GLY D:11 , LYS D:25 , GLN D:26 , GLN D:82 , PRO D:85 , ASP D:86 , GLY D:87 , LEU D:88 , LEU D:108 , ASP D:110 , ASN D:111 , TYR D:145 , GLY D:146 , GLU D:161 , LYS D:162 , VAL D:172 , GLU D:196 , THR D:200 , HOH D:3820 , HOH D:3958 , HOH D:3988 , HOH D:4107 , HOH D:4108
BINDING SITE FOR RESIDUE DAU D 3506
22
DC4
SOFTWARE
ILE B:216 , GLY B:218 , ARG B:219 , GLY B:220 , LEU D:45 , TYR D:114 , GLY D:115 , HIS D:116 , ASP D:117 , PHE D:118 , HIS D:119 , GLU D:120 , VAL D:250 , ALA D:251 , GLU D:255 , ILE D:256 , ARG D:259 , TYR D:293 , SO4 D:3819 , HOH D:3827 , HOH D:3833 , HOH D:3840 , HOH D:3857 , HOH D:3886 , HOH D:3892 , HOH D:3940
BINDING SITE FOR RESIDUE DAU D 3507
23
EC4
SOFTWARE
TYR A:31 , LYS A:249 , GLY A:279 , HOH A:3955 , HOH A:4205 , HOH A:4206 , HOH A:4221 , ARG B:15 , HIS B:229
BINDING SITE FOR RESIDUE CIT A 3800
24
EC5
SOFTWARE
HIS A:229 , HOH A:3905 , HOH A:3912 , HOH A:4063 , HOH A:4214 , HOH A:4215 , HOH A:4216 , HOH A:4217 , TYR B:31 , ASP B:32 , LYS B:249 , GLY B:279
BINDING SITE FOR RESIDUE CIT A 3801
[
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]
SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
Info
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1g1la_ (A:)
1b: SCOP_d1g1lc_ (C:)
1c: SCOP_d1g1ld_ (D:)
1d: SCOP_d1g1le_ (E:)
1e: SCOP_d1g1lf_ (F:)
1f: SCOP_d1g1lg_ (G:)
1g: SCOP_d1g1lh_ (H:)
1h: SCOP_d1g1lb_ (B:)
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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
:
RmlA (RfbA)
(27)
Pseudomonas aeruginosa [TaxId: 287]
(9)
1a
d1g1la_
A:
1b
d1g1lc_
C:
1c
d1g1ld_
D:
1d
d1g1le_
E:
1e
d1g1lf_
F:
1f
d1g1lg_
G:
1g
d1g1lh_
H:
1h
d1g1lb_
B:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1g1lA00 (A:2-293)
1b: CATH_1g1lD00 (D:2-293)
1c: CATH_1g1lE00 (E:2-293)
1d: CATH_1g1lG00 (G:2-293)
1e: CATH_1g1lH00 (H:2-293)
1f: CATH_1g1lB00 (B:1-293)
1g: CATH_1g1lF00 (F:1-293)
1h: CATH_1g1lC00 (C:2-293)
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Homologous Superfamily
:
Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
(231)
Pseudomonas aeruginosa. Organism_taxid: 287.
(7)
1a
1g1lA00
A:2-293
1b
1g1lD00
D:2-293
1c
1g1lE00
E:2-293
1d
1g1lG00
G:2-293
1e
1g1lH00
H:2-293
1f
1g1lB00
B:1-293
1g
1g1lF00
F:1-293
1h
1g1lC00
C:2-293
[
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Pfam Domains
(0, 0)
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