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2OBX
Asym. Unit
Info
Asym.Unit (242 KB)
Biol.Unit 1 (235 KB)
Biol.Unit 2 (120 KB)
Biol.Unit 3 (120 KB)
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(1)
Title
:
LUMAZINE SYNTHASE RIBH2 FROM MESORHIZOBIUM LOTI (GENE MLL7281, SWISS-PROT ENTRY Q986N2) COMPLEXED WITH INHIBITOR 5-NITRO-6-(D-RIBITYLAMINO)-2,4(1H,3H) PYRIMIDINEDIONE
Authors
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Br A. Bacher, M. Fischer, F. A. Goldbaum
Date
:
20 Dec 06 (Deposition) - 14 Aug 07 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.53
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Biol. Unit 2: A,B,C,D,E (1x)
Biol. Unit 3: F,G,H,I,J (1x)
Keywords
:
Lumazine Synthase, Alpha-Beta, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Klinke, V. Zylberman, H. R. Bonomi, I. Haase, B. G. Guimaraes, B. C. Braden, A. Bacher, M. Fischer, F. A. Goldbaum
Structural And Kinetic Properties Of Lumazine Synthase Isoenzymes In The Order Rhizobiales
J. Mol. Biol. V. 373 664 2007
[
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Hetero Components
(2, 19)
Info
All Hetero Components
1a: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIa)
1b: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIb)
1c: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIc)
1d: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INId)
1e: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIe)
1f: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIf)
1g: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIg)
1h: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIh)
1i: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIi)
1j: 5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)... (INIj)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
INI
10
Mod. Residue
5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
2
PO4
9
Ligand/Ion
PHOSPHATE ION
[
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Sites
(19, 19)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:83 , GLY A:84 , ILE A:85 , TYR A:86
BINDING SITE FOR RESIDUE PO4 A 1001
02
AC2
SOFTWARE
GLY B:83 , GLY B:84 , ILE B:85 , TYR B:86
BINDING SITE FOR RESIDUE PO4 B 1002
03
AC3
SOFTWARE
GLY C:83 , GLY C:84 , ILE C:85 , TYR C:86
BINDING SITE FOR RESIDUE PO4 C 1003
04
AC4
SOFTWARE
GLY E:83 , GLY E:84 , ILE E:85 , TYR E:86
BINDING SITE FOR RESIDUE PO4 E 1004
05
AC5
SOFTWARE
VAL F:81 , ASN F:82 , GLY F:83 , GLY F:84 , ILE F:85 , TYR F:86 , ARG F:87 , HIS F:88 , INI F:206
BINDING SITE FOR RESIDUE PO4 F 1005
06
AC6
SOFTWARE
ASN G:82 , GLY G:83 , GLY G:84 , ILE G:85 , TYR G:86
BINDING SITE FOR RESIDUE PO4 G 1006
07
AC7
SOFTWARE
ASN I:82 , GLY I:83 , GLY I:84 , ILE I:85 , TYR I:86 , HOH I:505
BINDING SITE FOR RESIDUE PO4 I 1007
08
AC8
SOFTWARE
GLY J:83 , GLY J:84 , ILE J:85 , TYR J:86
BINDING SITE FOR RESIDUE PO4 J 1008
09
AC9
SOFTWARE
ARG J:18
BINDING SITE FOR RESIDUE PO4 J 1009
10
BC1
SOFTWARE
TRP A:21 , GLY A:54 , ALA A:55 , TYR A:56 , GLU A:57 , PHE A:79 , VAL A:80 , VAL A:81 , LEU E:111 , SER E:112
BINDING SITE FOR RESIDUE INI A 201
11
BC2
SOFTWARE
LEU A:111 , SER A:112 , TRP B:21 , GLY B:54 , ALA B:55 , TYR B:56 , GLU B:57 , PHE B:79 , VAL B:80 , VAL B:81 , HOH B:321
BINDING SITE FOR RESIDUE INI B 202
12
BC3
SOFTWARE
LEU B:111 , SER B:112 , TRP C:21 , GLY C:54 , ALA C:55 , TYR C:56 , GLU C:57 , PHE C:79 , VAL C:80 , VAL C:81 , HOH C:331 , HOH C:342 , HOH C:343 , HOH C:473
BINDING SITE FOR RESIDUE INI C 203
13
BC4
SOFTWARE
LEU C:111 , SER C:112 , ALA D:19 , TRP D:21 , GLY D:54 , ALA D:55 , TYR D:56 , GLU D:57 , PHE D:79 , VAL D:80 , VAL D:81
BINDING SITE FOR RESIDUE INI D 204
14
BC5
SOFTWARE
LEU D:111 , SER D:112 , TRP E:21 , GLY E:54 , ALA E:55 , TYR E:56 , GLU E:57 , PHE E:79 , VAL E:80 , VAL E:81
BINDING SITE FOR RESIDUE INI E 205
15
BC6
SOFTWARE
TRP F:21 , HIS F:22 , GLY F:54 , ALA F:55 , TYR F:56 , GLU F:57 , PHE F:79 , VAL F:80 , VAL F:81 , PO4 F:1005 , LEU J:111 , SER J:112
BINDING SITE FOR RESIDUE INI F 206
16
BC7
SOFTWARE
LEU F:111 , SER F:112 , TRP G:21 , GLY G:54 , ALA G:55 , TYR G:56 , GLU G:57 , PHE G:79 , VAL G:80 , VAL G:81 , HOH G:403 , HOH G:407
BINDING SITE FOR RESIDUE INI G 207
17
BC8
SOFTWARE
LEU G:111 , SER G:112 , ALA H:19 , TRP H:21 , GLY H:54 , ALA H:55 , TYR H:56 , GLU H:57 , PHE H:79 , VAL H:80 , VAL H:81
BINDING SITE FOR RESIDUE INI H 208
18
BC9
SOFTWARE
LEU H:111 , SER H:112 , ALA I:19 , TRP I:21 , GLY I:54 , ALA I:55 , TYR I:56 , GLU I:57 , PHE I:79 , VAL I:80 , VAL I:81 , HOH I:442
BINDING SITE FOR RESIDUE INI I 209
19
CC1
SOFTWARE
LEU I:111 , SER I:112 , TRP J:21 , GLY J:54 , ALA J:55 , TYR J:56 , GLU J:57 , PHE J:79 , VAL J:80 , VAL J:81 , HOH J:458
BINDING SITE FOR RESIDUE INI J 210
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SAPs(SNPs)/Variants
(0, 0)
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(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, 10)
Info
All SCOP Domains
1a: SCOP_d2obxa_ (A:)
1b: SCOP_d2obxb_ (B:)
1c: SCOP_d2obxc_ (C:)
1d: SCOP_d2obxd_ (D:)
1e: SCOP_d2obxe_ (E:)
1f: SCOP_d2obxf_ (F:)
1g: SCOP_d2obxg_ (G:)
1h: SCOP_d2obxh_ (H:)
1i: SCOP_d2obxi_ (I:)
1j: SCOP_d2obxj_ (J:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Lumazine synthase
(27)
Superfamily
:
Lumazine synthase
(27)
Family
:
Lumazine synthase
(26)
Protein domain
:
automated matches
(7)
Mesorhizobium loti [TaxId: 381]
(1)
1a
d2obxa_
A:
1b
d2obxb_
B:
1c
d2obxc_
C:
1d
d2obxd_
D:
1e
d2obxe_
E:
1f
d2obxf_
F:
1g
d2obxg_
G:
1h
d2obxh_
H:
1i
d2obxi_
I:
1j
d2obxj_
J:
[
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CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_2obxA00 (A:6-155)
1b: CATH_2obxF00 (F:10-157)
1c: CATH_2obxG00 (G:10-157)
1d: CATH_2obxB00 (B:10-156)
1e: CATH_2obxC00 (C:10-156)
1f: CATH_2obxH00 (H:10-156)
1g: CATH_2obxD00 (D:10-155)
1h: CATH_2obxE00 (E:10-155)
1i: CATH_2obxI00 (I:10-155)
1j: CATH_2obxJ00 (J:10-155)
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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)
Mesorhizobium loti. Organism_taxid: 381.
(1)
1a
2obxA00
A:6-155
1b
2obxF00
F:10-157
1c
2obxG00
G:10-157
1d
2obxB00
B:10-156
1e
2obxC00
C:10-156
1f
2obxH00
H:10-156
1g
2obxD00
D:10-155
1h
2obxE00
E:10-155
1i
2obxI00
I:10-155
1j
2obxJ00
J:10-155
[
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Pfam Domains
(0, 0)
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