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2OBX
Biol. Unit 3
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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, 10)
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
5
Mod. Residue
5-NITRO-6-RIBITYL-AMINO-2,4(1H,3H)-PYRIMIDINEDIONE
2
PO4
5
Ligand/Ion
PHOSPHATE ION
[
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Sites
(10, 10)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC6 (SOFTWARE)
07: BC7 (SOFTWARE)
08: BC8 (SOFTWARE)
09: BC9 (SOFTWARE)
10: CC1 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
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
02
AC6
SOFTWARE
ASN G:82 , GLY G:83 , GLY G:84 , ILE G:85 , TYR G:86
BINDING SITE FOR RESIDUE PO4 G 1006
03
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
04
AC8
SOFTWARE
GLY J:83 , GLY J:84 , ILE J:85 , TYR J:86
BINDING SITE FOR RESIDUE PO4 J 1008
05
AC9
SOFTWARE
ARG J:18
BINDING SITE FOR RESIDUE PO4 J 1009
06
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
07
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
08
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
09
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
10
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 only available for the asymmetric unit)
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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.
(no "Exon" information available for biological units yet)
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
(
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(
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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
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Asymmetric Unit 1
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Asym.Unit (242 KB)
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Biol.Unit 1 (235 KB)
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Biol.Unit 3 (120 KB)
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