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2VI5
Biol. Unit 2
Info
Asym.Unit (244 KB)
Biol.Unit 1 (119 KB)
Biol.Unit 2 (119 KB)
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(1)
Title
:
LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO N-6-(RIBITYLAMINO)PYRIMIDINE-2,4(1H,3H)-DIONE-5-YL-PROPIONAMIDE
Authors
:
E. Morgunova, Y. Zhang, G. Jin, B. Illarionov, A. Bacher, M. Fischer, M. R. Ladenstein
Date
:
27 Nov 07 (Deposition) - 08 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Keywords
:
Transferase, Lumazine Synthase, Riboflavin Biosynthesis, Mycobacterium Tuberculosis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Zhang, B. Illarionov, E. Morgunova, A. Bacher, M. Fischer, R. Ladenstein, M. Cushman
A New Series Of N-[2, 4-Dioxo-6-D-Ribitylamino-1, 2, 3, 4-Tetrahydropyrimidin-5-Yl]Oxalamic Acid Derivatives As Inhibitors Of Lumazine Syntase And Riboflavin Synthase: Design, Synthesis, Biochemical Evaluation, Crystallography And Mechanistic Implications.
J. Org. Chem. V. 73 2715 2008
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
1i: POTASSIUM ION (Ki)
1j: POTASSIUM ION (Kj)
1k: POTASSIUM ION (Kk)
1l: POTASSIUM ION (Kl)
1m: POTASSIUM ION (Km)
1n: POTASSIUM ION (Kn)
1o: POTASSIUM ION (Ko)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
3a: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19a)
3b: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19b)
3c: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19c)
3d: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19d)
3e: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19e)
3f: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19f)
3g: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19g)
3h: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19h)
3i: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19i)
3j: 1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROP... (Y19j)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
PO4
5
Ligand/Ion
PHOSPHATE ION
3
Y19
5
Ligand/Ion
1-DEOXY-1-{[(5S)-2,6-DIOXO-5-(PROPANOYLAMINO)-1,2,5,6-TETRAHYDROPYRIMIDIN-4-YL]AMINO}-D-RIBITOL
[
close Hetero Component info
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Sites
(20, 20)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC7 (SOFTWARE)
03: BC2 (SOFTWARE)
04: BC6 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC6 (SOFTWARE)
10: CC7 (SOFTWARE)
11: CC8 (SOFTWARE)
12: CC9 (SOFTWARE)
13: DC1 (SOFTWARE)
14: DC2 (SOFTWARE)
15: DC3 (SOFTWARE)
16: DC4 (SOFTWARE)
17: DC5 (SOFTWARE)
18: DC6 (SOFTWARE)
19: DC7 (SOFTWARE)
20: DC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
GLU A:155 , LEU A:156 , ARG A:157 , HOH A:2085 , LEU J:156 , ARG J:157
BINDING SITE FOR RESIDUE K A 603
02
AC7
SOFTWARE
GLU B:155 , LEU B:156 , ARG B:157 , HOH B:2079 , GLU I:155 , LEU I:156 , ARG I:157
BINDING SITE FOR RESIDUE K B 603
03
BC2
SOFTWARE
GLU C:155 , LEU C:156 , ARG C:157 , LEU H:156 , ARG H:157
BINDING SITE FOR RESIDUE K C 603
04
BC6
SOFTWARE
GLU D:155 , LEU D:156 , ARG D:157 , LEU G:156 , ARG G:157 , HOH G:2050
BINDING SITE FOR RESIDUE K D 603
05
CC1
SOFTWARE
GLU E:155 , LEU E:156 , ARG E:157 , GLU F:155 , ARG F:157 , HOH F:2071
BINDING SITE FOR RESIDUE K E 603
06
CC3
SOFTWARE
TRP F:27 , GLY F:58 , ALA F:59 , ILE F:60 , GLU F:61 , VAL F:81 , VAL F:82 , ILE F:83 , HIS F:89 , PO4 F:702 , HOH F:2073 , HOH F:2074 , HOH F:2075 , HOH F:2076 , ALA G:113 , ASN G:114
BINDING SITE FOR RESIDUE Y19 F 201
07
CC4
SOFTWARE
ALA F:70 , HIS F:73 , THR F:110 , HOH F:2029
BINDING SITE FOR RESIDUE K F 601
08
CC5
SOFTWARE
GLY F:85 , GLN F:86 , THR F:87 , HIS F:89 , Y19 F:201 , HOH F:2035 , ARG G:128 , LYS G:138
BINDING SITE FOR RESIDUE PO4 F 702
09
CC6
SOFTWARE
TRP G:27 , GLY G:58 , ALA G:59 , ILE G:60 , GLU G:61 , VAL G:81 , VAL G:82 , ILE G:83 , HIS G:89 , PO4 G:702 , HOH G:2051 , HOH G:2052 , ALA H:113 , ASN H:114
BINDING SITE FOR RESIDUE Y19 G 201
10
CC7
SOFTWARE
ALA G:70 , HIS G:73 , THR G:110 , HOH G:2020 , HOH G:2021 , HOH G:2022
BINDING SITE FOR RESIDUE K G 601
11
CC8
SOFTWARE
GLY G:85 , GLN G:86 , THR G:87 , Y19 G:201 , HOH G:2051 , HOH G:2053 , ARG H:128
BINDING SITE FOR RESIDUE PO4 G 702
12
CC9
SOFTWARE
TRP H:27 , GLY H:58 , ALA H:59 , ILE H:60 , GLU H:61 , VAL H:81 , VAL H:82 , ILE H:83 , HIS H:89 , PO4 H:702 , HOH H:2077 , HOH H:2078 , HOH H:2079 , HOH H:2080 , ALA I:113 , ASN I:114 , HOH I:2062
BINDING SITE FOR RESIDUE Y19 H 201
13
DC1
SOFTWARE
ALA H:70 , HIS H:73 , THR H:110
BINDING SITE FOR RESIDUE K H 601
14
DC2
SOFTWARE
GLY H:85 , GLN H:86 , THR H:87 , Y19 H:201 , HOH H:2078 , HOH H:2080 , ARG I:128 , HOH I:2062
BINDING SITE FOR RESIDUE PO4 H 702
15
DC3
SOFTWARE
TRP I:27 , GLY I:58 , ALA I:59 , ILE I:60 , GLU I:61 , VAL I:81 , VAL I:82 , ILE I:83 , HIS I:89 , PO4 I:702 , HOH I:2071 , HOH I:2072 , HOH I:2073 , HOH I:2074 , HOH I:2075 , ALA J:113 , ASN J:114 , LYS J:138
BINDING SITE FOR RESIDUE Y19 I 201
16
DC4
SOFTWARE
ALA I:70 , HIS I:73 , THR I:110 , HOH I:2030 , HOH I:2048
BINDING SITE FOR RESIDUE K I 601
17
DC5
SOFTWARE
GLY I:85 , GLN I:86 , THR I:87 , Y19 I:201 , HOH I:2074 , HOH I:2075 , HOH I:2076 , HOH I:2077 , ARG J:128
BINDING SITE FOR RESIDUE PO4 I 702
18
DC6
SOFTWARE
ALA F:113 , ASN F:114 , LYS F:138 , TRP J:27 , GLY J:58 , ALA J:59 , ILE J:60 , GLU J:61 , VAL J:81 , VAL J:82 , ILE J:83 , HIS J:89 , PO4 J:702 , HOH J:2008 , HOH J:2098
BINDING SITE FOR RESIDUE Y19 J 201
19
DC7
SOFTWARE
ALA J:70 , HIS J:73 , THR J:110 , HOH J:2050 , HOH J:2075
BINDING SITE FOR RESIDUE K J 601
20
DC8
SOFTWARE
ARG F:128 , GLY J:85 , GLN J:86 , THR J:87 , Y19 J:201 , HOH J:2098 , HOH J:2099
BINDING SITE FOR RESIDUE PO4 J 702
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(0, 0)
Info
All SCOP Domains
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_2vi5E00 (E:10-160)
1b: CATH_2vi5A00 (A:11-160)
1c: CATH_2vi5I00 (I:11-160)
1d: CATH_2vi5D00 (D:13-160)
1e: CATH_2vi5H00 (H:13-160)
1f: CATH_2vi5B00 (B:14-160)
1g: CATH_2vi5F00 (F:14-160)
1h: CATH_2vi5G00 (G:14-160)
1i: CATH_2vi5C00 (C:15-160)
1j: CATH_2vi5J00 (J:15-160)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.960, no name defined]
(36)
Mycobacterium tuberculosis. Organism_taxid: 1773.
(8)
1a
2vi5E00
E:10-160
1b
2vi5A00
A:11-160
1c
2vi5I00
I:11-160
1d
2vi5D00
D:13-160
1e
2vi5H00
H:13-160
1f
2vi5B00
B:14-160
1g
2vi5F00
F:14-160
1h
2vi5G00
G:14-160
1i
2vi5C00
C:15-160
1j
2vi5J00
J:15-160
[
close CATH info
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Pfam Domains
(1, 10)
Info
all PFAM domains
1a: PFAM_DMRL_synthase_2vi5J01 (J:15-156)
1b: PFAM_DMRL_synthase_2vi5J02 (J:15-156)
1c: PFAM_DMRL_synthase_2vi5J03 (J:15-156)
1d: PFAM_DMRL_synthase_2vi5J04 (J:15-156)
1e: PFAM_DMRL_synthase_2vi5J05 (J:15-156)
1f: PFAM_DMRL_synthase_2vi5J06 (J:15-156)
1g: PFAM_DMRL_synthase_2vi5J07 (J:15-156)
1h: PFAM_DMRL_synthase_2vi5J08 (J:15-156)
1i: PFAM_DMRL_synthase_2vi5J09 (J:15-156)
1j: PFAM_DMRL_synthase_2vi5J10 (J:15-156)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DMRL_synthase]
(19)
Family
:
DMRL_synthase
(19)
Mycobacterium tuberculosis
(3)
1a
DMRL_synthase-2vi5J01
J:15-156
1b
DMRL_synthase-2vi5J02
J:15-156
1c
DMRL_synthase-2vi5J03
J:15-156
1d
DMRL_synthase-2vi5J04
J:15-156
1e
DMRL_synthase-2vi5J05
J:15-156
1f
DMRL_synthase-2vi5J06
J:15-156
1g
DMRL_synthase-2vi5J07
J:15-156
1h
DMRL_synthase-2vi5J08
J:15-156
1i
DMRL_synthase-2vi5J09
J:15-156
1j
DMRL_synthase-2vi5J10
J:15-156
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