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1G1L
Biol. Unit 2
Info
Asym.Unit (903 KB)
Biol.Unit 1 (452 KB)
Biol.Unit 2 (449 KB)
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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
(2, 20)
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
-1
Ligand/Ion
CITRIC ACID
2
DAU
8
Ligand/Ion
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
3
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC6 (SOFTWARE)
04: BC2 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC5 (SOFTWARE)
14: DC5 (SOFTWARE)
15: DC6 (SOFTWARE)
16: DC7 (SOFTWARE)
17: DC8 (SOFTWARE)
18: DC9 (SOFTWARE)
19: EC1 (SOFTWARE)
20: EC2 (SOFTWARE)
21: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
SER G:12 , GLY G:13 , THR G:14 , ARG G:15 , LYS G:25 , HOH G:3946 , HOH G:4117 , HOH G:4139 , HOH G:4157 , HOH G:4204
BINDING SITE FOR RESIDUE SO4 G 3702
02
AC4
SOFTWARE
SER H:12 , GLY H:13 , THR H:14 , ARG H:15
BINDING SITE FOR RESIDUE SO4 H 3703
03
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
04
BC2
SOFTWARE
ARG E:62 , HOH E:3885 , ARG F:62
BINDING SITE FOR RESIDUE SO4 E 3808
05
BC3
SOFTWARE
GLN E:127 , ARG E:128 , GLN E:129 , THR E:130 , HOH E:3980
BINDING SITE FOR RESIDUE SO4 E 3809
06
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
07
BC5
SOFTWARE
GLN F:129 , THR F:130
BINDING SITE FOR RESIDUE SO4 F 3811
08
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
09
BC7
SOFTWARE
GLU G:160 , GLU G:161 , ARG G:194 , ARG G:204 , HOH G:3880 , HOH G:3941 , HOH G:4134
BINDING SITE FOR RESIDUE SO4 G 3813
10
BC8
SOFTWARE
ARG G:62 , ARG H:62
BINDING SITE FOR RESIDUE SO4 H 3814
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
CC1
SOFTWARE
GLU H:160 , GLU H:161 , ARG H:204 , HOH H:3919 , HOH H:4149
BINDING SITE FOR RESIDUE SO4 H 3816
13
CC5
SOFTWARE
HIS E:116 , DAU E:3509 , HOH E:3831 , HOH E:3894 , HOH E:4034 , LEU H:121 , TYR H:221 , HOH H:3871
BINDING SITE FOR RESIDUE SO4 E 3820
14
DC5
SOFTWARE
LEU E:8 , GLY E:10 , GLY E:11 , LYS E:25 , GLN E:26 , GLN E:82 , PRO E:85 , ASP E:86 , GLY E:87 , LEU E:88 , LEU E:108 , ASP E:110 , ASN E:111 , TYR E:145 , GLY E:146 , GLU E:161 , LYS E:162 , VAL E:172 , GLU E:196 , THR E:200 , HOH E:3825 , HOH E:4126 , HOH E:4127 , HOH E:4128
BINDING SITE FOR RESIDUE DAU E 3508
15
DC6
SOFTWARE
LEU E:45 , TYR E:114 , GLY E:115 , HIS E:116 , ASP E:117 , PHE E:118 , HIS E:119 , GLU E:120 , VAL E:250 , ALA E:251 , GLU E:255 , ILE E:256 , TYR E:293 , SO4 E:3820 , HOH E:3827 , HOH E:3832 , HOH E:3833 , HOH E:3873 , HOH E:3894 , HOH E:3937 , ILE H:216 , GLY H:218 , ARG H:219 , GLY H:220
BINDING SITE FOR RESIDUE DAU E 3509
16
DC7
SOFTWARE
LEU F:8 , GLY F:10 , GLY F:11 , LYS F:25 , GLN F:26 , GLN F:82 , PRO F:85 , ASP F:86 , GLY F:87 , LEU F:88 , LEU F:108 , ASP F:110 , ASN F:111 , TYR F:145 , GLY F:146 , GLU F:161 , LYS F:162 , VAL F:172 , ARG F:194 , GLU F:196 , THR F:200 , TRP F:223 , HOH F:3828 , HOH F:3922 , HOH F:3990 , HOH F:4001 , HOH F:4118 , HOH F:4119
BINDING SITE FOR RESIDUE DAU F 3510
17
DC8
SOFTWARE
LEU F:45 , TYR F:114 , GLY F:115 , HIS F:116 , ASP F:117 , PHE F:118 , HIS F:119 , GLU F:120 , VAL F:250 , ALA F:251 , GLU F:255 , ILE F:256 , TYR F:293 , HOH F:3818 , HOH F:3826 , HOH F:3832 , HOH F:3876 , HOH F:3878 , HOH F:3926 , ILE G:216 , GLY G:218 , ARG G:219 , GLY G:220
BINDING SITE FOR RESIDUE DAU F 3511
18
DC9
SOFTWARE
LEU H:8 , GLY H:10 , GLY H:11 , GLN H:26 , GLN H:82 , PRO H:85 , ASP H:86 , GLY H:87 , LEU H:88 , LEU H:108 , ASP H:110 , ASN H:111 , TYR H:145 , GLY H:146 , GLU H:161 , LYS H:162 , VAL H:172 , THR H:200 , HOH H:3825 , HOH H:3884 , HOH H:4002 , HOH H:4068 , HOH H:4139 , HOH H:4193
BINDING SITE FOR RESIDUE DAU H 3512
19
EC1
SOFTWARE
ILE E:216 , GLY E:218 , ARG E:219 , GLY E:220 , LEU H:45 , TYR H:114 , GLY H:115 , HIS H:116 , ASP H:117 , PHE H:118 , HIS H:119 , GLU H:120 , VAL H:250 , ALA H:251 , GLU H:255 , ILE H:256 , ARG H:259 , TYR H:293 , HOH H:3832 , HOH H:3835 , HOH H:3851 , HOH H:3905 , HOH H:3908 , HOH H:3914 , HOH H:3949 , HOH H:3952 , HOH H:4076
BINDING SITE FOR RESIDUE DAU H 3513
20
EC2
SOFTWARE
LEU G:8 , GLY G:10 , GLY G:11 , GLN G:26 , GLN G:82 , PRO G:85 , ASP G:86 , GLY G:87 , LEU G:88 , LEU G:108 , GLY G:109 , ASP G:110 , ASN G:111 , TYR G:145 , GLY G:146 , GLU G:161 , LYS G:162 , VAL G:172 , THR G:200 , HOH G:3827 , HOH G:3895 , HOH G:3902 , HOH G:3965 , HOH G:3990 , HOH G:4052 , HOH G:4117 , HOH G:4126 , HOH G:4157
BINDING SITE FOR RESIDUE DAU G 3514
21
EC3
SOFTWARE
ILE F:216 , GLY F:218 , ARG F:219 , GLY F:220 , LEU G:45 , TYR G:114 , GLY G:115 , HIS G:116 , ASP G:117 , PHE G:118 , HIS G:119 , GLU G:120 , VAL G:250 , ALA G:251 , GLU G:255 , ILE G:256 , ARG G:259 , TYR G:293 , HOH G:3823 , HOH G:3829 , HOH G:3856 , HOH G:3879 , HOH G:3891 , HOH G:3907 , HOH G:3997 , HOH G:4142
BINDING SITE FOR RESIDUE DAU G 3515
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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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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(
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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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Asym.Unit (903 KB)
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