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2AF6
Asym. Unit
Info
Asym.Unit (354 KB)
Biol.Unit 1 (173 KB)
Biol.Unit 10 (91 KB)
Biol.Unit 2 (173 KB)
Biol.Unit 3 (90 KB)
Biol.Unit 4 (90 KB)
Biol.Unit 5 (90 KB)
Biol.Unit 6 (90 KB)
Biol.Unit 7 (90 KB)
Biol.Unit 8 (90 KB)
Biol.Unit 9 (90 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS FLAVIN DEPENDENT THYMIDYLATE SYNTHASE (MTB THYX) IN THE PRESENCE OF CO-FACTOR FAD AND SUBSTRATE ANALOG 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE (BRDUMP)
Authors
:
P. Sampathkumar, S. Turley, J. E. Ulmer, H. G. Rhie, C. H. Sibley, W. G. Ho
Date
:
25 Jul 05 (Deposition) - 04 Oct 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.01
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)
Biol. Unit 3: F,H (1x)
Biol. Unit 4: E,G (1x)
Biol. Unit 5: B,D (1x)
Biol. Unit 6: A,C (1x)
Biol. Unit 7: E,H (1x)
Biol. Unit 8: B,C (1x)
Biol. Unit 9: F,G (1x)
Biol. Unit 10: A,D (1x)
Keywords
:
M. Tuberculosis, Thyx, Fdts, Tscp, Flavin Dependent Thymidylate Synthase, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Sampathkumar, S. Turley, J. E. Ulmer, H. G. Rhie, C. H. Sibley, W. G. Hol
Structure Of The Mycobacterium Tuberculosis Flavin Dependen Thymidylate Synthase (Mtbthyx) At 2. 0A Resolution.
J. Mol. Biol. V. 352 1091 2005
[
close entry info
]
Hetero Components
(5, 72)
Info
All Hetero Components
1a: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUa)
1b: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUb)
1c: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUc)
1d: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUd)
1e: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUe)
1f: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUf)
1g: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUg)
1h: 5-BROMO-2'-DEOXYURIDINE-5'-MONOPHO... (BRUh)
2a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
2b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
2c: FLAVIN-ADENINE DINUCLEOTIDE (FADc)
2d: FLAVIN-ADENINE DINUCLEOTIDE (FADd)
2e: FLAVIN-ADENINE DINUCLEOTIDE (FADe)
2f: FLAVIN-ADENINE DINUCLEOTIDE (FADf)
2g: FLAVIN-ADENINE DINUCLEOTIDE (FADg)
2h: FLAVIN-ADENINE DINUCLEOTIDE (FADh)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
4a: IODIDE ION (IODa)
4b: IODIDE ION (IODb)
4c: IODIDE ION (IODc)
4d: IODIDE ION (IODd)
4e: IODIDE ION (IODe)
4f: IODIDE ION (IODf)
4g: IODIDE ION (IODg)
4h: IODIDE ION (IODh)
4i: IODIDE ION (IODi)
4j: IODIDE ION (IODj)
5a: SELENOMETHIONINE (MSEa)
5aa: SELENOMETHIONINE (MSEaa)
5ab: SELENOMETHIONINE (MSEab)
5ac: SELENOMETHIONINE (MSEac)
5ad: SELENOMETHIONINE (MSEad)
5ae: SELENOMETHIONINE (MSEae)
5af: SELENOMETHIONINE (MSEaf)
5b: SELENOMETHIONINE (MSEb)
5c: SELENOMETHIONINE (MSEc)
5d: SELENOMETHIONINE (MSEd)
5e: SELENOMETHIONINE (MSEe)
5f: SELENOMETHIONINE (MSEf)
5g: SELENOMETHIONINE (MSEg)
5h: SELENOMETHIONINE (MSEh)
5i: SELENOMETHIONINE (MSEi)
5j: SELENOMETHIONINE (MSEj)
5k: SELENOMETHIONINE (MSEk)
5l: SELENOMETHIONINE (MSEl)
5m: SELENOMETHIONINE (MSEm)
5n: SELENOMETHIONINE (MSEn)
5o: SELENOMETHIONINE (MSEo)
5p: SELENOMETHIONINE (MSEp)
5q: SELENOMETHIONINE (MSEq)
5r: SELENOMETHIONINE (MSEr)
5s: SELENOMETHIONINE (MSEs)
5t: SELENOMETHIONINE (MSEt)
5u: SELENOMETHIONINE (MSEu)
5v: SELENOMETHIONINE (MSEv)
5w: SELENOMETHIONINE (MSEw)
5x: SELENOMETHIONINE (MSEx)
5y: SELENOMETHIONINE (MSEy)
5z: SELENOMETHIONINE (MSEz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BRU
8
Mod. Residue
5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2
FAD
8
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
3
GOL
14
Ligand/Ion
GLYCEROL
4
IOD
10
Ligand/Ion
IODIDE ION
5
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(40, 40)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:247 , HOH A:4737
BINDING SITE FOR RESIDUE IOD A 3001
02
AC2
SOFTWARE
FAD C:2600 , PHE D:70 , SER D:71 , GOL D:2012
BINDING SITE FOR RESIDUE IOD D 3002
03
AC3
SOFTWARE
THR G:54 , HOH G:6715
BINDING SITE FOR RESIDUE IOD G 3003
04
AC4
SOFTWARE
TYR D:189 , VAL D:222 , HOH D:3122 , HOH D:3123 , HOH D:3124
BINDING SITE FOR RESIDUE IOD D 3004
05
AC5
SOFTWARE
LYS F:14 , THR F:15 , GLY F:32 , TYR F:189 , VAL F:222 , HOH F:7704
BINDING SITE FOR RESIDUE IOD F 3005
06
AC6
SOFTWARE
VAL E:23 , GLN G:10
BINDING SITE FOR RESIDUE IOD E 3006
07
AC7
SOFTWARE
THR E:4
BINDING SITE FOR RESIDUE IOD E 3007
08
AC8
SOFTWARE
THR A:4
BINDING SITE FOR RESIDUE IOD A 3008
09
AC9
SOFTWARE
THR C:4
BINDING SITE FOR RESIDUE IOD C 3009
10
BC1
SOFTWARE
ARG F:41 , PRO F:50 , THR F:54 , GOL F:2014 , HOH F:7707
BINDING SITE FOR RESIDUE IOD F 3010
11
BC2
SOFTWARE
SER A:102 , GLN A:103 , SER A:105 , CYS C:43 , SER C:71 , GLU C:74 , HIS C:98 , ASN C:188 , ARG C:190 , FAD C:2600 , ARG D:95 , HIS D:96 , ARG D:97 , HIS D:98 , HIS D:194 , MSE D:198 , ARG D:199 , HIS D:203 , BRU D:1603 , HOH D:3026 , HOH D:3040 , HOH D:3050 , HOH D:3054
BINDING SITE FOR RESIDUE FAD D 1600
12
BC3
SOFTWARE
ARG A:87 , GLN A:103 , LEU A:104 , SER A:105 , GLN A:106 , ARG A:107 , ARG A:172 , HIS D:91 , GLU D:92 , ARG D:95 , ARG D:199 , FAD D:1600 , HOH D:3014 , HOH D:3019
BINDING SITE FOR RESIDUE BRU D 1603
13
BC4
SOFTWARE
SER B:102 , GLN B:103 , SER B:105 , HOH B:3689 , ARG C:95 , HIS C:96 , ARG C:97 , HIS C:98 , HIS C:194 , MSE C:198 , ARG C:199 , HIS C:203 , BRU C:2603 , HOH C:3060 , HOH C:3074 , HOH C:3076 , HOH C:3078 , CYS D:43 , SER D:71 , GLU D:74 , HIS D:98 , ASN D:188 , ARG D:190 , FAD D:1600 , GOL D:2012 , IOD D:3002
BINDING SITE FOR RESIDUE FAD C 2600
14
BC5
SOFTWARE
ARG B:87 , GLN B:103 , LEU B:104 , SER B:105 , GLN B:106 , ARG B:107 , TYR B:108 , ARG B:172 , HIS C:91 , GLU C:92 , ARG C:95 , ARG C:199 , FAD C:2600 , HOH C:3015 , HOH C:3021
BINDING SITE FOR RESIDUE BRU C 2603
15
BC6
SOFTWARE
CYS A:43 , SER A:71 , GLU A:74 , HIS A:98 , ASN A:188 , ARG A:190 , GOL A:2013 , FAD A:4600 , ARG B:95 , HIS B:96 , ARG B:97 , HIS B:98 , HIS B:194 , MSE B:198 , ARG B:199 , HIS B:203 , BRU B:3603 , HOH B:3647 , HOH B:3660 , HOH B:3723 , SER C:102 , GLN C:103 , SER C:105 , TYR C:108 , HOH C:3073
BINDING SITE FOR RESIDUE FAD B 3600
16
BC7
SOFTWARE
HIS B:91 , GLU B:92 , ARG B:95 , ARG B:199 , FAD B:3600 , HOH B:3604 , HOH B:3615 , ARG C:87 , GLN C:103 , LEU C:104 , SER C:105 , GLN C:106 , ARG C:107 , TYR C:108 , ARG C:172
BINDING SITE FOR RESIDUE BRU B 3603
17
BC8
SOFTWARE
ARG A:95 , HIS A:96 , ARG A:97 , HIS A:98 , HIS A:194 , MSE A:198 , ARG A:199 , HIS A:203 , BRU A:4603 , HOH A:4627 , HOH A:4636 , HOH A:4647 , HOH A:4701 , HOH A:4726 , HOH A:4731 , CYS B:43 , SER B:71 , GLU B:74 , HIS B:98 , ASN B:188 , ARG B:190 , FAD B:3600 , SER D:102 , GLN D:103 , TYR D:108
BINDING SITE FOR RESIDUE FAD A 4600
18
BC9
SOFTWARE
HIS A:91 , GLU A:92 , ARG A:95 , ARG A:199 , FAD A:4600 , HOH A:4606 , HOH A:4634 , ARG D:87 , GLN D:103 , LEU D:104 , SER D:105 , GLN D:106 , ARG D:107 , TYR D:108 , ARG D:172
BINDING SITE FOR RESIDUE BRU A 4603
19
CC1
SOFTWARE
SER E:102 , GLN E:103 , TYR E:108 , HOH E:8648 , HOH E:8676 , CYS G:43 , SER G:71 , HIS G:98 , ASN G:188 , ARG G:190 , FAD G:6600 , ARG H:95 , HIS H:96 , ARG H:97 , HIS H:98 , HIS H:194 , MSE H:198 , ARG H:199 , HIS H:203 , BRU H:5603 , HOH H:5664 , HOH H:5670 , HOH H:5689
BINDING SITE FOR RESIDUE FAD H 5600
20
CC2
SOFTWARE
ARG E:87 , GLN E:103 , LEU E:104 , SER E:105 , GLN E:106 , ARG E:107 , TYR E:108 , ARG E:172 , HIS H:91 , GLU H:92 , ARG H:95 , ARG H:199 , FAD H:5600 , HOH H:5606 , HOH H:5614
BINDING SITE FOR RESIDUE BRU H 5603
21
CC3
SOFTWARE
SER F:102 , GLN F:103 , SER F:105 , HOH F:7634 , HOH F:7690 , ARG G:95 , HIS G:96 , ARG G:97 , HIS G:98 , HIS G:194 , MSE G:198 , ARG G:199 , BRU G:6603 , HOH G:6656 , HOH G:6658 , CYS H:43 , SER H:71 , GLU H:74 , HIS H:98 , ASN H:188 , ARG H:190 , FAD H:5600
BINDING SITE FOR RESIDUE FAD G 6600
22
CC4
SOFTWARE
ARG F:87 , GLN F:103 , LEU F:104 , SER F:105 , GLN F:106 , ARG F:107 , TYR F:108 , ARG F:172 , HIS G:91 , GLU G:92 , ARG G:95 , ARG G:199 , FAD G:6600 , HOH G:6607 , HOH G:6624
BINDING SITE FOR RESIDUE BRU G 6603
23
CC5
SOFTWARE
CYS E:43 , SER E:71 , GLU E:74 , HIS E:98 , ASN E:188 , ARG E:190 , FAD E:8600 , ARG F:95 , HIS F:96 , ARG F:97 , HIS F:98 , HIS F:194 , MSE F:198 , ARG F:199 , HIS F:203 , BRU F:7603 , HOH F:7624 , HOH F:7653 , HOH F:7659 , HOH F:7696 , SER G:102 , GLN G:103 , SER G:105 , TYR G:108 , HOH G:6706
BINDING SITE FOR RESIDUE FAD F 7600
24
CC6
SOFTWARE
HIS F:91 , GLU F:92 , ARG F:95 , ARG F:199 , FAD F:7600 , HOH F:7606 , HOH F:7613 , ARG G:87 , GLN G:103 , LEU G:104 , SER G:105 , GLN G:106 , ARG G:107 , TYR G:108 , ARG G:172
BINDING SITE FOR RESIDUE BRU F 7603
25
CC7
SOFTWARE
ARG E:95 , HIS E:96 , ARG E:97 , HIS E:98 , HIS E:194 , MSE E:198 , ARG E:199 , HIS E:203 , BRU E:8603 , HOH E:8661 , HOH E:8666 , HOH E:8688 , CYS F:43 , SER F:71 , GLU F:74 , HIS F:98 , ASN F:188 , ARG F:190 , GOL F:2007 , FAD F:7600 , SER H:102 , GLN H:103 , SER H:105
BINDING SITE FOR RESIDUE FAD E 8600
26
CC8
SOFTWARE
HIS E:91 , GLU E:92 , ARG E:95 , ARG E:199 , FAD E:8600 , HOH E:8604 , HOH E:8605 , ARG H:87 , GLN H:103 , LEU H:104 , SER H:105 , GLN H:106 , ARG H:107 , TYR H:108 , ARG H:172
BINDING SITE FOR RESIDUE BRU E 8603
27
CC9
SOFTWARE
LYS A:14 , THR A:15 , GLY A:32 , SER A:77 , VAL A:78 , TYR A:189 , HOH A:4702
BINDING SITE FOR RESIDUE GOL A 2001
28
DC1
SOFTWARE
LYS B:14 , THR B:15 , GLY B:31 , GLY B:32 , SER B:77 , VAL B:78 , TYR B:189 , VAL B:222
BINDING SITE FOR RESIDUE GOL B 2002
29
DC2
SOFTWARE
LYS C:14 , THR C:15 , GLY C:31 , GLY C:32 , SER C:77 , VAL C:78 , TYR C:189 , VAL C:222 , HOH C:3093
BINDING SITE FOR RESIDUE GOL C 2003
30
DC3
SOFTWARE
LYS E:14 , THR E:15 , GLY E:31 , GLY E:32 , SER E:77 , VAL E:78 , TYR E:189 , VAL E:222
BINDING SITE FOR RESIDUE GOL E 2004
31
DC4
SOFTWARE
LYS G:14 , THR G:15 , GLY G:32 , SER G:77 , VAL G:78 , TYR G:189 , VAL G:222 , HOH G:6691
BINDING SITE FOR RESIDUE GOL G 2005
32
DC5
SOFTWARE
LYS H:14 , THR H:15 , GLY H:31 , GLY H:32 , SER H:77 , TYR H:189 , VAL H:222 , HOH H:5605
BINDING SITE FOR RESIDUE GOL H 2006
33
DC6
SOFTWARE
FAD E:8600 , HIS F:69 , SER F:71 , HOH F:7689
BINDING SITE FOR RESIDUE GOL F 2007
34
DC7
SOFTWARE
LEU B:216 , ARG B:217 , PHE B:227 , PHE B:230 , HOH B:3617 , HOH B:3645 , SER F:48 , LYS F:49 , PRO F:50
BINDING SITE FOR RESIDUE GOL B 2008
35
DC8
SOFTWARE
ARG D:41 , PRO D:50 , THR D:54 , TYR D:60
BINDING SITE FOR RESIDUE GOL D 2009
36
DC9
SOFTWARE
ARG A:41 , THR A:54 , TYR A:60
BINDING SITE FOR RESIDUE GOL A 2010
37
EC1
SOFTWARE
ARG E:87 , HIS E:91 , ASN E:177 , ARG H:87 , SER H:88 , HIS H:91 , ASN H:177
BINDING SITE FOR RESIDUE GOL E 2011
38
EC2
SOFTWARE
FAD C:2600 , HIS D:69 , SER D:71 , VAL D:72 , IOD D:3002 , HOH D:3025 , HOH D:3117
BINDING SITE FOR RESIDUE GOL D 2012
39
EC3
SOFTWARE
HIS A:69 , SER A:71 , VAL A:72 , HOH A:4619 , HOH A:4727 , FAD B:3600
BINDING SITE FOR RESIDUE GOL A 2013
40
EC4
SOFTWARE
ARG F:41 , PRO F:50 , THR F:54 , IOD F:3010 , HOH F:7645 , HOH F:7706 , HOH F:7707
BINDING SITE FOR RESIDUE GOL F 2014
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: THYX (A:7-233,B:7-233,C:7-233,D:7-233,E:...)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THYX
PS51331
Flavin-dependent thymidylate synthase (thyX) domain profile.
THYX_MYCTO
7-233
8
A:7-233
B:7-233
C:7-233
D:7-233
E:7-233
F:7-233
G:7-233
H:7-233
THYX_MYCTU
7-233
8
A:7-233
B:7-233
C:7-233
D:7-233
E:7-233
F:7-233
G:7-233
H:7-233
[
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Asym.Unit (354 KB)
Header - Asym.Unit
Biol.Unit 1 (173 KB)
Header - Biol.Unit 1
Biol.Unit 10 (91 KB)
Header - Biol.Unit 10
Biol.Unit 2 (173 KB)
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Biol.Unit 3 (90 KB)
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