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4FZB
Asym. Unit
Info
Asym.Unit (555 KB)
Biol.Unit 1 (142 KB)
Biol.Unit 2 (141 KB)
Biol.Unit 3 (140 KB)
Biol.Unit 4 (140 KB)
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(1)
Title
:
STRUCTURE OF THYMIDYLATE SYNTHASE THYX COMPLEXED TO A NEW INHIBITOR
Authors
:
T. Basta, Y. Boum, J. Briffotaux, H. F. Becker, I. Lamarre-Jouenne, J. C S. Skouloubris, U. Liebl, H. Van Tilbeurgh, M. Graille, H. Myllylkal
Date
:
06 Jul 12 (Deposition) - 22 May 13 (Release) - 06 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.59
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Homotetramer, Fad-Dependent Thymidylate Synthase, Transferase- Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Basta, Y. Boum, J. Briffotaux, H. F. Becker, I. Lamarre-Jouenne, J. C. Lambry, S. Skouloubris, U. Liebl, M. Graille, H. Van Tilbeurgh, H. Myllykallio
Mechanistic And Structural Basis For Inhibition Of Thymidylate Synthase Thyx.
Open Biology V. 2 20120 2012
[
close entry info
]
Hetero Components
(3, 45)
Info
All Hetero Components
1a: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJa)
1b: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJb)
1c: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJc)
1d: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJd)
1e: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJe)
1f: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJf)
1g: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJg)
1h: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJh)
1i: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJi)
1j: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJj)
1k: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJk)
1l: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJl)
1m: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJm)
1n: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJn)
1o: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJo)
1p: 2-HYDROXY-3-(4-METHOXYBENZYL)NAPHT... (0VJp)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
2g: DIMETHYL SULFOXIDE (DMSg)
2h: DIMETHYL SULFOXIDE (DMSh)
2i: DIMETHYL SULFOXIDE (DMSi)
2j: DIMETHYL SULFOXIDE (DMSj)
2k: DIMETHYL SULFOXIDE (DMSk)
2l: DIMETHYL SULFOXIDE (DMSl)
2m: DIMETHYL SULFOXIDE (DMSm)
3a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
3b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
3c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
3d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
3e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
3f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
3g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
3h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
3i: FLAVIN-ADENINE DINUCLEOTIDE (FADi)
3j: FLAVIN-ADENINE DINUCLEOTIDE (FADj)
3k: FLAVIN-ADENINE DINUCLEOTIDE (FADk)
3l: FLAVIN-ADENINE DINUCLEOTIDE (FADl)
3m: FLAVIN-ADENINE DINUCLEOTIDE (FADm)
3n: FLAVIN-ADENINE DINUCLEOTIDE (FADn)
3o: FLAVIN-ADENINE DINUCLEOTIDE (FADo)
3p: FLAVIN-ADENINE DINUCLEOTIDE (FADp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0VJ
16
Ligand/Ion
2-HYDROXY-3-(4-METHOXYBENZYL)NAPHTHALENE-1,4-DIONE
2
DMS
13
Ligand/Ion
DIMETHYL SULFOXIDE
3
FAD
16
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(45, 45)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:54 , ARG A:78 , HIS A:79 , ARG A:80 , SER A:81 , ARG A:173 , ASP A:174 , HIS A:177 , LEU A:181 , ARG A:182 , FAD A:302 , 0VJ A:303 , HOH A:402 , HOH A:403 , GLN C:85 , GLU C:86 , SER C:88 , SER D:30 , ASN D:31 , HIS D:51 , HIS D:53 , TRP D:54 , SER D:55 , GLU D:58 , ARG D:173
BINDING SITE FOR RESIDUE FAD A 301
02
AC2
SOFTWARE
ASN A:31 , HIS A:51 , HIS A:53 , TRP A:54 , SER A:55 , ARG A:173 , FAD A:301 , HOH A:407 , GLN B:85 , GLU B:86 , SER B:88 , 0VJ B:303 , ARG D:78 , HIS D:79 , ARG D:80 , SER D:81 , ARG D:173 , ASP D:174 , HIS D:177 , ARG D:182
BINDING SITE FOR RESIDUE FAD A 302
03
AC3
SOFTWARE
GLN A:75 , ARG A:78 , ARG A:182 , GLY A:186 , GLN A:188 , FAD A:301 , GLU C:86 , PHE C:87 , SER C:88 , GLN C:89 , ARG C:90
BINDING SITE FOR RESIDUE 0VJ A 303
04
AC4
SOFTWARE
GLN A:85 , PHE A:87 , THR A:165 , TYR A:167 , VAL B:29
BINDING SITE FOR RESIDUE DMS A 304
05
AC5
SOFTWARE
GLU A:86 , PHE A:87 , SER A:88 , GLN A:89 , ARG A:90 , GLU A:152 , GLN C:75 , ARG C:78 , ARG C:182 , GLY C:186 , GLN C:188 , FAD C:301
BINDING SITE FOR RESIDUE 0VJ A 305
06
AC6
SOFTWARE
TRP B:54 , ARG B:78 , HIS B:79 , ARG B:80 , SER B:81 , ARG B:173 , ASP B:174 , HIS B:177 , ARG B:182 , SER C:30 , ASN C:31 , HIS C:53 , TRP C:54 , SER C:55 , ARG C:173 , FAD C:301 , GLN D:85 , GLU D:86 , SER D:88 , 0VJ D:301
BINDING SITE FOR RESIDUE FAD B 301
07
AC7
SOFTWARE
GLN B:85 , PHE B:87 , THR B:165 , ILE B:166 , TYR B:167
BINDING SITE FOR RESIDUE DMS B 302
08
AC8
SOFTWARE
FAD A:302 , PHE B:87 , SER B:88 , GLN B:89 , ARG B:90 , GLU B:152 , GLN D:75 , ARG D:78 , ARG D:182 , GLY D:186 , GLN D:188
BINDING SITE FOR RESIDUE 0VJ B 303
09
AC9
SOFTWARE
GLN A:85 , GLU A:86 , SER A:88 , 0VJ A:305 , SER B:30 , HIS B:51 , HIS B:53 , TRP B:54 , SER B:55 , ARG B:173 , FAD B:301 , TRP C:54 , ARG C:78 , HIS C:79 , ARG C:80 , SER C:81 , ARG C:173 , ASP C:174 , HIS C:177
BINDING SITE FOR RESIDUE FAD C 301
10
BC1
SOFTWARE
GLN C:85 , GLU C:86 , PHE C:87 , THR C:165 , VAL D:29
BINDING SITE FOR RESIDUE DMS C 302
11
BC2
SOFTWARE
ALA B:74 , GLN B:75 , ARG B:78 , ARG B:182 , GLY B:186 , GLN B:188 , FAD B:301 , GLU D:86 , PHE D:87 , SER D:88 , GLN D:89 , ARG D:90 , GLU D:152
BINDING SITE FOR RESIDUE 0VJ D 301
12
BC3
SOFTWARE
VAL C:29 , SER C:30 , GLN D:85 , GLU D:86 , PHE D:87 , THR D:165 , TYR D:167
BINDING SITE FOR RESIDUE DMS D 302
13
BC4
SOFTWARE
TRP E:54 , ARG E:78 , HIS E:79 , ARG E:80 , SER E:81 , ARG E:173 , ASP E:174 , HIS E:177 , ARG E:182 , 0VJ E:302 , GLN G:85 , GLU G:86 , SER G:88 , SER H:30 , HIS H:51 , HIS H:53 , TRP H:54 , SER H:55 , ARG H:173 , FAD H:302
BINDING SITE FOR RESIDUE FAD E 301
14
BC5
SOFTWARE
GLN E:75 , ARG E:78 , ARG E:182 , GLY E:186 , GLN E:188 , FAD E:301 , GLU G:86 , PHE G:87 , SER G:88 , GLN G:89 , ARG G:90 , GLU G:152
BINDING SITE FOR RESIDUE 0VJ E 302
15
BC6
SOFTWARE
GLN E:85 , GLU E:86 , PHE E:87 , THR E:165 , TYR E:167
BINDING SITE FOR RESIDUE DMS E 303
16
BC7
SOFTWARE
ARG F:78 , HIS F:79 , ARG F:80 , SER F:81 , ARG F:173 , ASP F:174 , HIS F:177 , LEU F:181 , ARG F:182 , FAD F:302 , HOH F:412 , ASN G:31 , HIS G:51 , HIS G:53 , TRP G:54 , SER G:55 , ARG G:173 , HOH G:410 , GLN H:85 , GLU H:86 , SER H:88 , 0VJ H:301
BINDING SITE FOR RESIDUE FAD F 301
17
BC8
SOFTWARE
GLN E:85 , GLU E:86 , ASN F:31 , HIS F:51 , HIS F:53 , TRP F:54 , SER F:55 , ARG F:173 , FAD F:301 , TRP G:54 , ARG G:78 , HIS G:79 , ARG G:80 , SER G:81 , ARG G:173 , ASP G:174 , HIS G:177 , LEU G:181 , 0VJ G:301
BINDING SITE FOR RESIDUE FAD F 302
18
BC9
SOFTWARE
VAL E:29 , GLN F:85 , GLU F:86 , PHE F:87 , THR F:165 , TYR F:167
BINDING SITE FOR RESIDUE DMS F 303
19
CC1
SOFTWARE
GLU F:86 , PHE F:87 , SER F:88 , GLN F:89 , ARG F:90 , GLU F:152 , GLN H:75 , ARG H:182 , GLY H:186 , GLN H:188 , FAD H:302
BINDING SITE FOR RESIDUE 0VJ F 304
20
CC2
SOFTWARE
GLU E:86 , PHE E:87 , SER E:88 , GLN E:89 , ARG E:90 , FAD F:302 , GLN G:75 , ARG G:78 , ARG G:182 , GLY G:186 , GLN G:188
BINDING SITE FOR RESIDUE 0VJ G 301
21
CC3
SOFTWARE
GLN G:85 , THR G:165 , VAL H:29
BINDING SITE FOR RESIDUE DMS G 302
22
CC4
SOFTWARE
GLN F:75 , ARG F:78 , ARG F:182 , GLY F:186 , GLN F:188 , FAD F:301 , GLU H:86 , PHE H:87 , SER H:88 , GLN H:89 , ARG H:90 , GLU H:152
BINDING SITE FOR RESIDUE 0VJ H 301
23
CC5
SOFTWARE
SER E:30 , ASN E:31 , HIS E:51 , HIS E:53 , TRP E:54 , SER E:55 , ARG E:173 , FAD E:301 , GLN F:85 , GLU F:86 , SER F:88 , 0VJ F:304 , TRP H:54 , ARG H:78 , HIS H:79 , ARG H:80 , SER H:81 , ARG H:173 , ASP H:174 , HIS H:177 , LEU H:181 , ARG H:182 , HOH H:405
BINDING SITE FOR RESIDUE FAD H 302
24
CC6
SOFTWARE
GLN H:85 , PHE H:87 , THR H:165 , TYR H:167
BINDING SITE FOR RESIDUE DMS H 303
25
CC7
SOFTWARE
TRP I:54 , ARG I:78 , HIS I:79 , ARG I:80 , SER I:81 , ARG I:173 , ASP I:174 , HIS I:177 , ARG I:182 , FAD I:302 , HOH I:402 , GLN K:85 , GLU K:86 , SER K:88 , 0VJ K:301 , ASN L:31 , HIS L:51 , HIS L:53 , TRP L:54 , SER L:55 , ARG L:173 , HOH L:401
BINDING SITE FOR RESIDUE FAD I 301
26
CC8
SOFTWARE
SER I:30 , HIS I:51 , HIS I:53 , TRP I:54 , SER I:55 , ARG I:173 , FAD I:301 , GLN J:85 , GLU J:86 , SER J:88 , TRP L:54 , ARG L:78 , HIS L:79 , ARG L:80 , SER L:81 , ARG L:173 , ASP L:174 , HIS L:177 , ARG L:182 , 0VJ L:301 , HOH L:406
BINDING SITE FOR RESIDUE FAD I 302
27
CC9
SOFTWARE
GLN I:85 , THR I:165 , ILE I:166 , TYR I:167 , VAL J:29
BINDING SITE FOR RESIDUE DMS I 303
28
DC1
SOFTWARE
GLU I:86 , PHE I:87 , SER I:88 , GLN I:89 , ARG I:90 , GLU I:152 , ARG K:78 , ARG K:182 , GLY K:186 , GLN K:188 , FAD K:302
BINDING SITE FOR RESIDUE 0VJ I 304
29
DC2
SOFTWARE
TRP J:54 , ARG J:78 , HIS J:79 , ARG J:80 , SER J:81 , ARG J:173 , ASP J:174 , HIS J:177 , LEU J:181 , ARG J:182 , 0VJ J:302 , ASN K:31 , HIS K:51 , LYS K:52 , HIS K:53 , TRP K:54 , SER K:55 , ARG K:173 , FAD K:302 , GLN L:85 , GLU L:86 , SER L:88
BINDING SITE FOR RESIDUE FAD J 301
30
DC3
SOFTWARE
GLN J:75 , ARG J:78 , ARG J:182 , GLY J:186 , GLN J:188 , FAD J:301 , GLU L:86 , PHE L:87 , SER L:88 , GLN L:89 , ARG L:90 , GLU L:152
BINDING SITE FOR RESIDUE 0VJ J 302
31
DC4
SOFTWARE
ARG I:78 , ARG I:182 , GLY I:186 , GLN I:188 , FAD I:301 , GLU K:86 , PHE K:87 , SER K:88 , GLN K:89 , ARG K:90 , GLU K:152
BINDING SITE FOR RESIDUE 0VJ K 301
32
DC5
SOFTWARE
GLN I:85 , GLU I:86 , SER I:88 , 0VJ I:304 , SER J:30 , HIS J:51 , HIS J:53 , TRP J:54 , SER J:55 , ARG J:173 , FAD J:301 , HOH J:405 , TRP K:54 , ARG K:78 , HIS K:79 , ARG K:80 , SER K:81 , ARG K:173 , ASP K:174 , HIS K:177 , ARG K:182
BINDING SITE FOR RESIDUE FAD K 302
33
DC6
SOFTWARE
GLN K:85 , GLU K:86 , PHE K:87 , THR K:165 , TYR K:167 , SER L:30
BINDING SITE FOR RESIDUE DMS K 303
34
DC7
SOFTWARE
FAD I:302 , GLU J:86 , PHE J:87 , SER J:88 , GLN J:89 , ARG J:90 , GLU J:152 , GLN L:75 , ARG L:78 , ARG L:182 , GLY L:186 , GLN L:188
BINDING SITE FOR RESIDUE 0VJ L 301
35
DC8
SOFTWARE
TRP M:54 , ARG M:78 , HIS M:79 , ARG M:80 , SER M:81 , ARG M:173 , ASP M:174 , HIS M:177 , ARG M:182 , GLN O:85 , GLU O:86 , SER O:88 , 0VJ O:301 , ASN P:31 , HIS P:51 , HIS P:53 , TRP P:54 , SER P:55 , ARG P:173 , FAD P:301
BINDING SITE FOR RESIDUE FAD M 301
36
DC9
SOFTWARE
GLN M:85 , GLU M:86 , THR M:165 , ILE M:166 , TYR M:167
BINDING SITE FOR RESIDUE DMS M 302
37
EC1
SOFTWARE
GLU M:86 , PHE M:87 , SER M:88 , GLN M:89 , ARG M:90 , GLU M:152 , GLN O:75 , ARG O:78 , ARG O:182 , GLY O:186 , GLN O:188 , FAD O:302
BINDING SITE FOR RESIDUE 0VJ M 303
38
EC2
SOFTWARE
TRP N:54 , ARG N:78 , HIS N:79 , ARG N:80 , SER N:81 , ARG N:173 , ASP N:174 , HIS N:177 , LEU N:181 , 0VJ N:302 , ASN O:31 , HIS O:51 , HIS O:53 , TRP O:54 , SER O:55 , ARG O:173 , FAD O:302 , GLN P:85 , GLU P:86 , SER P:88
BINDING SITE FOR RESIDUE FAD N 301
39
EC3
SOFTWARE
GLN N:75 , ARG N:78 , ARG N:182 , GLY N:186 , GLN N:188 , FAD N:301 , GLU P:86 , PHE P:87 , SER P:88 , GLN P:89 , ARG P:90 , GLU P:152
BINDING SITE FOR RESIDUE 0VJ N 302
40
EC4
SOFTWARE
GLN M:75 , ARG M:78 , ARG M:182 , GLY M:186 , GLN M:188 , FAD M:301 , GLU O:86 , PHE O:87 , SER O:88 , GLN O:89 , ARG O:90 , GLU O:152
BINDING SITE FOR RESIDUE 0VJ O 301
41
EC5
SOFTWARE
GLN M:85 , GLU M:86 , SER M:88 , 0VJ M:303 , SER N:30 , HIS N:51 , HIS N:53 , TRP N:54 , SER N:55 , ARG N:173 , FAD N:301 , ARG O:78 , HIS O:79 , SER O:81 , ARG O:173 , ASP O:174 , HIS O:177 , LEU O:181 , ARG O:182
BINDING SITE FOR RESIDUE FAD O 302
42
EC6
SOFTWARE
GLN O:85 , PHE O:87 , THR O:165 , TYR O:167 , VAL P:29 , SER P:30
BINDING SITE FOR RESIDUE DMS O 303
43
EC7
SOFTWARE
SER M:30 , HIS M:51 , HIS M:53 , TRP M:54 , SER M:55 , ARG M:173 , FAD M:301 , GLN N:85 , GLU N:86 , SER N:88 , TRP P:54 , ARG P:78 , HIS P:79 , ARG P:80 , SER P:81 , ARG P:173 , ASP P:174 , HIS P:177 , ARG P:182 , 0VJ P:302
BINDING SITE FOR RESIDUE FAD P 301
44
EC8
SOFTWARE
GLU N:86 , PHE N:87 , SER N:88 , GLN N:89 , ARG N:90 , GLU N:152 , GLN P:75 , ARG P:78 , ARG P:182 , GLY P:186 , GLN P:188 , FAD P:301
BINDING SITE FOR RESIDUE 0VJ P 302
45
EC9
SOFTWARE
SER O:30 , GLN P:85 , PHE P:87 , THR P:165 , TYR P:167
BINDING SITE FOR RESIDUE DMS P 303
[
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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all CATH domains
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Pfam Domains
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all PFAM domains
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Atom Selection
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all
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All Atoms
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Protein & NOT PROSITE
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Chain J
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Asymmetric Unit 1
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Miscellaneous
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Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
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Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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