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Asym. Unit
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (287 KB)
Biol.Unit 2 (286 KB)
Biol.Unit 3 (285 KB)
Biol.Unit 4 (278 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E.COLI THYMIDYLATE SYNTHASE WITH DUMP AND THE BGC 945 INHIBITOR
Authors
:
A. Tochowicz, J. Finer-Moore, R. M. Stroud
Date
:
16 Jan 13 (Deposition) - 25 Dec 13 (Release) - 12 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: C,F (1x)
Biol. Unit 4: G,H (1x)
Keywords
:
Alpha/Beta Protein, Methylase, Methyltransferase, Dump Subtrate, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Tochowicz, S. Dalziel, O. Eidam, J. D. O'Connell, S. Griner, J. S. Finer-Moore, R. M. Stroud
Development And Binding Mode Assessment Of N-[4-[2-Propyn-1-Yl[(6S)-4, 6, 7, 8-Tetrahydro-2- (Hydroxymethyl)-4-Oxo-3H-Cyclopenta[G]Quinazolin-6- Yl]Amino]Benzoyl]-L-Gamma-Glutamyl-D-Glutamic Acid (Bgc 945), A Novel Thymidylate Synthase Inhibitor That Targets Tumor Cells.
J. Med. Chem. V. 56 5446 2013
[
close entry info
]
Hetero Components
(5, 31)
Info
All Hetero Components
1a: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYa)
1b: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYb)
1c: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYc)
1d: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYd)
1e: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYe)
1f: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYf)
1g: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYg)
1h: N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OX... (1JYh)
2a: N-CARBOXYMETHIONINE (CXMa)
2b: N-CARBOXYMETHIONINE (CXMb)
2c: N-CARBOXYMETHIONINE (CXMc)
2d: N-CARBOXYMETHIONINE (CXMd)
2e: N-CARBOXYMETHIONINE (CXMe)
2f: N-CARBOXYMETHIONINE (CXMf)
2g: N-CARBOXYMETHIONINE (CXMg)
2h: N-CARBOXYMETHIONINE (CXMh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
4a: 2'-DEOXY-5'-URIDYLIC ACID (UMCa)
4b: 2'-DEOXY-5'-URIDYLIC ACID (UMCb)
4c: 2'-DEOXY-5'-URIDYLIC ACID (UMCc)
4d: 2'-DEOXY-5'-URIDYLIC ACID (UMCd)
4e: 2'-DEOXY-5'-URIDYLIC ACID (UMCe)
5a: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMPa)
5b: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMPb)
5c: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMPc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1JY
8
Ligand/Ion
N-(4-{[(6S)-2-(HYDROXYMETHYL)-4-OXO-4,6,7,8-TETRAHYDRO-1H-CYCLOPENTA[G]QUINAZOLIN-6-YL](PROP-2-YN-1-YL)AMINO}BENZOYL)-L-GAMMA-GLUTAMYL-D-GLUTAMIC ACID
2
CXM
8
Mod. Amino Acid
N-CARBOXYMETHIONINE
3
MG
7
Ligand/Ion
MAGNESIUM ION
4
UMC
5
Ligand/Ion
2'-DEOXY-5'-URIDYLIC ACID
5
UMP
3
Ligand/Ion
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:21 , CYS A:146 , HIS A:147 , GLN A:165 , ARG A:166 , SER A:167 , CYS A:168 , ASP A:169 , GLY A:173 , ASN A:177 , HIS A:207 , TYR A:209 , 1JY A:303 , HOH A:405 , HOH A:418 , HOH A:470 , ARG E:126
BINDING SITE FOR RESIDUE UMP A 301
02
AC2
SOFTWARE
HOH A:579 , HOH A:580 , HOH A:581 , HOH A:582 , HOH A:583 , HOH A:584
BINDING SITE FOR RESIDUE MG A 302
03
AC3
SOFTWARE
HIS A:51 , GLU A:58 , ILE A:79 , TRP A:80 , TRP A:83 , ASP A:169 , LEU A:172 , GLY A:173 , PHE A:176 , ASN A:177 , TYR A:209 , VAL A:262 , ALA A:263 , UMP A:301 , HOH A:423 , HOH A:432 , HOH A:442 , HOH A:463 , HOH A:473 , HOH A:476 , HOH A:477 , HOH A:505 , HOH A:550 , HOH A:579 , HOH A:580 , HOH A:582 , HOH C:459
BINDING SITE FOR RESIDUE 1JY A 303
04
AC4
SOFTWARE
ARG B:21 , CYS B:146 , HIS B:147 , GLN B:165 , ARG B:166 , SER B:167 , CYS B:168 , ASP B:169 , ASN B:177 , HIS B:207 , TYR B:209 , 1JY B:303 , HOH B:415 , HOH B:499 , HOH B:527 , HOH B:528 , ARG D:126
BINDING SITE FOR RESIDUE UMC B 301
05
AC5
SOFTWARE
HOH B:564 , HOH B:565 , HOH B:566 , HOH B:567 , HOH B:568 , HOH B:569
BINDING SITE FOR RESIDUE MG B 302
06
AC6
SOFTWARE
HIS B:51 , GLU B:58 , ILE B:79 , TRP B:80 , TRP B:83 , LEU B:143 , ASP B:169 , LEU B:172 , GLY B:173 , PHE B:176 , ASN B:177 , TYR B:209 , VAL B:262 , ALA B:263 , UMC B:301 , HOH B:425 , HOH B:431 , HOH B:436 , HOH B:437 , HOH B:449 , HOH B:469 , HOH B:523 , HOH B:565 , HOH B:566 , HOH B:569
BINDING SITE FOR RESIDUE 1JY B 303
07
AC7
SOFTWARE
ARG C:21 , CYS C:146 , HIS C:147 , GLN C:165 , ARG C:166 , SER C:167 , CYS C:168 , ASP C:169 , ASN C:177 , HIS C:207 , TYR C:209 , 1JY C:303 , HOH C:414 , ARG F:126 , ARG F:127
BINDING SITE FOR RESIDUE UMP C 301
08
AC8
SOFTWARE
HOH C:563 , HOH C:564 , HOH C:565 , HOH C:566 , HOH C:567 , HOH C:568
BINDING SITE FOR RESIDUE MG C 302
09
AC9
SOFTWARE
PRO A:256 , HIS C:51 , ILE C:79 , TRP C:80 , TRP C:83 , LEU C:143 , ASP C:169 , LEU C:172 , GLY C:173 , PHE C:176 , ASN C:177 , TYR C:209 , VAL C:262 , ALA C:263 , UMP C:301 , HOH C:404 , HOH C:406 , HOH C:410 , HOH C:413 , HOH C:432 , HOH C:445 , HOH C:518 , HOH C:564 , HOH C:566 , HOH C:567 , HOH C:568
BINDING SITE FOR RESIDUE 1JY C 303
10
BC1
SOFTWARE
ARG B:126 , ARG B:127 , ARG D:21 , CYS D:146 , HIS D:147 , GLN D:165 , ARG D:166 , SER D:167 , CYS D:168 , ASP D:169 , GLY D:173 , ASN D:177 , HIS D:207 , TYR D:209 , 1JY D:303 , HOH D:436
BINDING SITE FOR RESIDUE UMC D 301
11
BC2
SOFTWARE
HOH D:526 , HOH D:527 , HOH D:528 , HOH D:529 , HOH D:530 , HOH D:531
BINDING SITE FOR RESIDUE MG D 302
12
BC3
SOFTWARE
HIS D:51 , GLU D:58 , ILE D:79 , TRP D:80 , TRP D:83 , ASP D:169 , LEU D:172 , GLY D:173 , PHE D:176 , ASN D:177 , TYR D:209 , VAL D:262 , ALA D:263 , UMC D:301 , HOH D:406 , HOH D:413 , HOH D:429 , HOH D:437 , HOH D:441 , HOH D:442 , HOH D:492 , HOH D:499 , HOH D:525 , HOH D:526 , HOH D:528 , HOH D:529 , HOH E:440 , HOH E:488
BINDING SITE FOR RESIDUE 1JY D 303
13
BC4
SOFTWARE
ARG A:126 , ARG E:21 , CYS E:146 , HIS E:147 , GLN E:165 , ARG E:166 , SER E:167 , CYS E:168 , ASP E:169 , ASN E:177 , HIS E:207 , TYR E:209 , 1JY E:303 , HOH E:409 , HOH E:436
BINDING SITE FOR RESIDUE UMC E 301
14
BC5
SOFTWARE
THR E:78 , HOH E:525 , HOH E:526 , HOH E:527 , HOH E:528 , HOH E:529
BINDING SITE FOR RESIDUE MG E 302
15
BC6
SOFTWARE
PRO D:256 , HIS E:51 , SER E:54 , GLU E:58 , THR E:78 , ILE E:79 , TRP E:80 , TRP E:83 , ASP E:169 , LEU E:172 , GLY E:173 , PHE E:176 , ASN E:177 , TYR E:209 , VAL E:262 , ALA E:263 , UMC E:301 , HOH E:421 , HOH E:426 , HOH E:458 , HOH E:484 , HOH E:511 , HOH E:527 , HOH E:528
BINDING SITE FOR RESIDUE 1JY E 303
16
BC7
SOFTWARE
ARG C:126 , ARG F:21 , CYS F:146 , HIS F:147 , GLN F:165 , ARG F:166 , SER F:167 , CYS F:168 , ASP F:169 , ASN F:177 , HIS F:207 , TYR F:209 , 1JY F:302 , HOH F:423
BINDING SITE FOR RESIDUE UMC F 301
17
BC8
SOFTWARE
HIS F:51 , ILE F:79 , TRP F:83 , ASP F:169 , LEU F:172 , GLY F:173 , PHE F:176 , ASN F:177 , TYR F:209 , VAL F:262 , ALA F:263 , UMC F:301 , PRO H:256 , GLY H:257 , ILE H:258
BINDING SITE FOR RESIDUE 1JY F 302
18
BC9
SOFTWARE
ARG G:21 , CYS G:146 , HIS G:147 , GLN G:165 , ARG G:166 , SER G:167 , CYS G:168 , ASP G:169 , GLY G:173 , ASN G:177 , HIS G:207 , TYR G:209 , 1JY G:303 , HOH G:425 , ARG H:126
BINDING SITE FOR RESIDUE UMP G 301
19
CC1
SOFTWARE
HOH G:469 , HOH G:470 , HOH G:471 , HOH G:472 , HOH G:473 , HOH G:474
BINDING SITE FOR RESIDUE MG G 302
20
CC2
SOFTWARE
PRO B:256 , HIS G:51 , GLU G:58 , THR G:78 , ILE G:79 , TRP G:80 , TRP G:83 , ASP G:169 , LEU G:172 , GLY G:173 , PHE G:176 , ASN G:177 , TYR G:209 , VAL G:262 , ALA G:263 , UMP G:301 , HOH G:409 , HOH G:413 , HOH G:418 , HOH G:422 , HOH G:430 , HOH G:435 , HOH G:471 , HOH G:473 , HOH G:474
BINDING SITE FOR RESIDUE 1JY G 303
21
CC3
SOFTWARE
ARG G:126 , ARG H:21 , CYS H:146 , HIS H:147 , GLN H:165 , ARG H:166 , SER H:167 , CYS H:168 , ASP H:169 , ASN H:177 , HIS H:207 , TYR H:209 , 1JY H:303 , HOH H:432
BINDING SITE FOR RESIDUE UMC H 301
22
CC4
SOFTWARE
HOH H:448 , HOH H:449 , HOH H:450 , HOH H:451 , HOH H:452 , HOH H:453
BINDING SITE FOR RESIDUE MG H 302
23
CC5
SOFTWARE
LYS F:259 , GLU H:58 , ILE H:79 , TRP H:80 , TRP H:83 , ASP H:169 , LEU H:172 , GLY H:173 , PHE H:176 , ASN H:177 , TYR H:209 , VAL H:262 , ALA H:263 , UMC H:301 , HOH H:414 , HOH H:416 , HOH H:420 , HOH H:450 , HOH H:452 , HOH H:453
BINDING SITE FOR RESIDUE 1JY H 303
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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_d4iska_ (A:)
1b: SCOP_d4iskb_ (B:)
1c: SCOP_d4iskc_ (C:)
1d: SCOP_d4iskd_ (D:)
1e: SCOP_d4iske_ (E:)
1f: SCOP_d4iskf_ (F:)
1g: SCOP_d4iskg_ (G:)
1h: SCOP_d4iskh_ (H:)
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Protein Domains
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Thymidylate synthase/dCMP hydroxymethylase
(193)
Superfamily
:
Thymidylate synthase/dCMP hydroxymethylase
(193)
Family
:
Thymidylate synthase/dCMP hydroxymethylase
(183)
Protein domain
:
Thymidylate synthase
(137)
Escherichia coli [TaxId: 562]
(64)
1a
d4iska_
A:
1b
d4iskb_
B:
1c
d4iskc_
C:
1d
d4iskd_
D:
1e
d4iske_
E:
1f
d4iskf_
F:
1g
d4iskg_
G:
1h
d4iskh_
H:
[
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CATH Domains
(0, 0)
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Pfam Domains
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Asym.Unit (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (287 KB)
Header - Biol.Unit 1
Biol.Unit 2 (286 KB)
Header - Biol.Unit 2
Biol.Unit 3 (285 KB)
Header - Biol.Unit 3
Biol.Unit 4 (278 KB)
Header - Biol.Unit 4
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