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1LVW
Asym. Unit
Info
Asym.Unit (219 KB)
Biol.Unit 1 (212 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE, RMLA, COMPLEX WITH DTDP
Authors
:
A. Dong, D. Christendat, E. F. Pai, Northeast Structural Genomics C (Nesg)
Date
:
29 May 02 (Deposition) - 29 Jul 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Protein Nucleotide Complex, Nucleotide Binding Fold, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Dong, D. Christendat, E. F. Pai
Crystal Structure Of Glucose-1-Phosphate Thymidylyltransferase, Rmla, Complex With Dtdp
To Be Published
[
close entry info
]
Hetero Components
(4, 26)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
4a: THYMIDINE-5'-DIPHOSPHATE (TYDa)
4b: THYMIDINE-5'-DIPHOSPHATE (TYDb)
4c: THYMIDINE-5'-DIPHOSPHATE (TYDc)
4d: THYMIDINE-5'-DIPHOSPHATE (TYDd)
4e: THYMIDINE-5'-DIPHOSPHATE (TYDe)
4f: THYMIDINE-5'-DIPHOSPHATE (TYDf)
4g: THYMIDINE-5'-DIPHOSPHATE (TYDg)
4h: THYMIDINE-5'-DIPHOSPHATE (TYDh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
5
Ligand/Ion
CHLORIDE ION
2
GOL
11
Ligand/Ion
GLYCEROL
3
SO4
2
Ligand/Ion
SULFATE ION
4
TYD
8
Ligand/Ion
THYMIDINE-5'-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:198 , ASN A:201 , HOH A:1053
BINDING SITE FOR RESIDUE CL A 4001
02
AC2
SOFTWARE
THR B:198 , ASN B:201 , HOH B:1151
BINDING SITE FOR RESIDUE CL B 4002
03
AC3
SOFTWARE
THR C:198 , ASN C:201 , HOH C:1247 , HOH C:1250
BINDING SITE FOR RESIDUE CL C 4003
04
AC4
SOFTWARE
THR D:198 , ASN D:201
BINDING SITE FOR RESIDUE CL D 4004
05
AC5
SOFTWARE
LYS A:165 , HOH A:1444 , ASP B:149 , SER B:150 , HIS C:291
BINDING SITE FOR RESIDUE CL C 4005
06
AC6
SOFTWARE
SER A:199 , ARG A:206 , HOH A:1176 , HOH A:1302
BINDING SITE FOR RESIDUE SO4 A 5001
07
AC7
SOFTWARE
THR C:262 , ARG C:263 , GLU C:264 , HOH C:1727 , TYR D:256 , ARG D:263 , HOH D:1202
BINDING SITE FOR RESIDUE SO4 D 5002
08
AC8
SOFTWARE
LEU A:6 , GLY A:8 , LYS A:23 , GLN A:24 , GLN A:80 , PRO A:83 , ARG A:84 , GLY A:85 , LEU A:106 , GLY A:107 , ASP A:108 , GLU A:194 , HOH A:1618 , HOH A:1619 , GOL A:2007
BINDING SITE FOR RESIDUE TYD A 3001
09
AC9
SOFTWARE
LEU A:43 , TYR A:112 , GLY A:113 , HIS A:114 , ARG A:115 , PHE A:116 , SER A:117 , ILE A:248 , ALA A:249 , GLU A:253 , ILE A:254 , HOH A:1007 , HOH A:1023 , HOH A:1026 , HOH A:1035 , HOH A:1048 , HOH A:1190 , HOH A:1315 , ARG C:217
BINDING SITE FOR RESIDUE TYD A 3002
10
BC1
SOFTWARE
LEU B:6 , GLY B:8 , GLY B:9 , LYS B:23 , GLN B:24 , GLN B:80 , PRO B:83 , ARG B:84 , GLY B:85 , LEU B:106 , ASP B:108 , GLU B:194 , HOH B:1683
BINDING SITE FOR RESIDUE TYD B 3003
11
BC2
SOFTWARE
LEU B:43 , TYR B:112 , GLY B:113 , HIS B:114 , ARG B:115 , PHE B:116 , SER B:117 , ILE B:248 , ALA B:249 , GLU B:253 , ILE B:254 , HOH B:1002 , HOH B:1013 , HOH B:1043 , HOH B:1055 , HOH B:1102 , HOH B:1129 , HOH B:1570 , ARG D:217
BINDING SITE FOR RESIDUE TYD B 3004
12
BC3
SOFTWARE
LEU C:6 , GLY C:8 , GLY C:9 , LYS C:23 , GLN C:24 , GLN C:80 , PRO C:83 , ARG C:84 , GLY C:85 , LEU C:106 , ASP C:108 , GOL C:2003
BINDING SITE FOR RESIDUE TYD C 3005
13
BC4
SOFTWARE
ARG A:217 , HOH A:1078 , LEU C:43 , TYR C:112 , GLY C:113 , HIS C:114 , ARG C:115 , PHE C:116 , SER C:117 , ILE C:248 , ALA C:249 , ILE C:254 , HOH C:1011 , HOH C:1018 , HOH C:1069 , HOH C:1081 , HOH C:1091 , HOH C:1093 , HOH C:1405
BINDING SITE FOR RESIDUE TYD C 3006
14
BC5
SOFTWARE
LEU D:6 , GLY D:8 , GLY D:9 , LYS D:23 , GLN D:24 , GLN D:80 , PRO D:83 , ARG D:84 , GLY D:85 , LEU D:106 , ASP D:108 , GOL D:2004
BINDING SITE FOR RESIDUE TYD D 3007
15
BC6
SOFTWARE
ARG B:217 , HOH B:1107 , LEU D:43 , TYR D:112 , GLY D:113 , HIS D:114 , ARG D:115 , PHE D:116 , SER D:117 , ILE D:248 , ALA D:249 , ILE D:254 , HOH D:1037 , HOH D:1060 , HOH D:1075 , HOH D:1089 , HOH D:1217 , HOH D:1427 , HOH D:1645
BINDING SITE FOR RESIDUE TYD D 3008
16
BC7
SOFTWARE
LYS A:242 , ARG A:243 , GLY A:245 , ARG C:138 , ASP C:139 , HOH C:1178 , HOH C:1293 , GOL C:2010
BINDING SITE FOR RESIDUE GOL C 2001
17
BC8
SOFTWARE
ARG B:138 , ASP B:139 , HOH B:1307 , HOH B:1697 , LYS D:242 , ARG D:243 , GLY D:245
BINDING SITE FOR RESIDUE GOL B 2002
18
BC9
SOFTWARE
LYS C:23 , ASP C:108 , LEU C:222 , ASP C:223 , THR C:224 , GLY C:225 , GOL C:2010 , TYD C:3005
BINDING SITE FOR RESIDUE GOL C 2003
19
CC1
SOFTWARE
GOL B:2011 , LYS D:23 , ASP D:108 , LEU D:222 , ASP D:223 , THR D:224 , GLY D:225 , TYD D:3007
BINDING SITE FOR RESIDUE GOL D 2004
20
CC2
SOFTWARE
ARG A:138 , ASP A:139 , PHE A:143 , HOH A:1294 , LYS C:242 , ARG C:243 , GLY C:245
BINDING SITE FOR RESIDUE GOL A 2005
21
CC3
SOFTWARE
LYS B:242 , ARG B:243 , GLY B:245 , ARG D:138 , ASP D:139 , PHE D:143 , HOH D:1297 , HOH D:1536
BINDING SITE FOR RESIDUE GOL D 2006
22
CC4
SOFTWARE
LYS A:23 , ASP A:108 , LEU A:222 , ASP A:223 , THR A:224 , GLY A:225 , HOH A:1015 , HOH A:1206 , TYD A:3001 , HOH C:1591
BINDING SITE FOR RESIDUE GOL A 2007
23
CC5
SOFTWARE
GLU B:151 , GLY B:152 , VAL B:212 , GLU B:213 , HOH B:1295
BINDING SITE FOR RESIDUE GOL B 2008
24
CC6
SOFTWARE
GLU A:147 , PHE A:148 , LYS A:165 , SER A:166 , HOH A:1034
BINDING SITE FOR RESIDUE GOL A 2009
25
CC7
SOFTWARE
ARG A:243 , PHE C:143 , TRP C:221 , LEU C:222 , ASP C:223 , HOH C:1178 , HOH C:1544 , GOL C:2001 , GOL C:2003
BINDING SITE FOR RESIDUE GOL C 2010
26
CC8
SOFTWARE
ARG B:243 , HOH B:1700 , TRP D:221 , LEU D:222 , HOH D:1536 , GOL D:2004
BINDING SITE FOR RESIDUE GOL B 2011
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1lvwa_ (A:)
1b: SCOP_d1lvwb_ (B:)
1c: SCOP_d1lvwc_ (C:)
1d: SCOP_d1lvwd_ (D:)
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Classes
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(
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Folds
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(
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Superfamilies
(
)
(
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Families
(
)
(
)
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)
Methanobacterium thermoautotrophicum [TaxId: 145262]
(1)
1a
d1lvwa_
A:
1b
d1lvwb_
B:
1c
d1lvwc_
C:
1d
d1lvwd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1lvwD00 (D:0-292)
1b: CATH_1lvwB00 (B:0-291)
1c: CATH_1lvwC00 (C:-1-292)
1d: CATH_1lvwA00 (A:-2-292)
View:
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Topologies
(
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(
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Homologous Superfamilies
(
)
(
)
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)
Methanothermobacter thermautotrophicus. Organism_taxid: 145262.
(1)
1a
1lvwD00
D:0-292
1b
1lvwB00
B:0-291
1c
1lvwC00
C:-1-292
1d
1lvwA00
A:-2-292
[
close CATH info
]
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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Sidechain
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Protein & NOT Site
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Chain D
Asymmetric Unit 1
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Asym.Unit (219 KB)
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