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1KYV
Biol. Unit 1
Info
Asym.Unit (127 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (239 KB)
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(1)
Title
:
LUMAZINE SYNTHASE FROM S.POMBE BOUND TO RIBOFLAVIN
Authors
:
S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bach R. Huber, M. Fischer
Date
:
06 Feb 02 (Deposition) - 24 Jul 02 (Release) - 23 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: A,B,C,D,E (2x)
Keywords
:
Riboflavin Biosynthesis, Lumazine Synthase, Schizosaccharomyces Pombe, Ligand Binding, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Gerhardt, I. Haase, S. Steinbacher, J. T. Kaiser, M. Cushman, A. Bacher, R. Huber, M. Fischer
The Structural Basis Of Riboflavin Binding To Schizosaccharomyces Pombe 6, 7-Dimethyl-8-Ribityllumazine Synthase.
J. Mol. Biol. V. 318 1317 2002
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Hetero Components
(2, 10)
Info
All Hetero Components
1a: PHOSPHATE ION (PO4a)
1b: PHOSPHATE ION (PO4b)
1c: PHOSPHATE ION (PO4c)
1d: PHOSPHATE ION (PO4d)
1e: PHOSPHATE ION (PO4e)
2a: RIBOFLAVIN (RBFa)
2b: RIBOFLAVIN (RBFb)
2c: RIBOFLAVIN (RBFc)
2d: RIBOFLAVIN (RBFd)
2e: RIBOFLAVIN (RBFe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PO4
5
Ligand/Ion
PHOSPHATE ION
2
RBF
5
Ligand/Ion
RIBOFLAVIN
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:133 , GLY B:90 , SER B:91 , THR B:92 , RBF B:502 , HOH B:1005 , HOH B:1014
BINDING SITE FOR RESIDUE PO4 B 1001
02
AC2
SOFTWARE
ARG D:133 , GLY E:90 , SER E:91 , THR E:92 , HIS E:94 , RBF E:505 , HOH E:1003
BINDING SITE FOR RESIDUE PO4 E 1002
03
AC3
SOFTWARE
ARG B:133 , GLY C:90 , SER C:91 , THR C:92 , RBF C:503 , HOH C:1004 , HOH C:1024
BINDING SITE FOR RESIDUE PO4 C 1003
04
AC4
SOFTWARE
GLY A:90 , SER A:91 , THR A:92 , RBF A:501 , ARG E:133
BINDING SITE FOR RESIDUE PO4 A 1004
05
AC5
SOFTWARE
ARG C:133 , GLY D:90 , SER D:91 , THR D:92 , RBF D:504 , HOH D:1006
BINDING SITE FOR RESIDUE PO4 D 1005
06
AC6
SOFTWARE
TRP A:27 , GLY A:61 , SER A:62 , TRP A:63 , GLU A:64 , VAL A:86 , LEU A:87 , ILE A:88 , HIS A:94 , ILE A:98 , PO4 A:1004 , HOH A:1005 , ILE E:118 , LEU E:119 , HIS E:142
BINDING SITE FOR RESIDUE RBF A 501
07
AC7
SOFTWARE
ILE A:118 , LEU A:119 , HIS A:142 , TRP A:146 , TRP B:27 , GLY B:61 , SER B:62 , TRP B:63 , GLU B:64 , VAL B:86 , LEU B:87 , ILE B:88 , HIS B:94 , PO4 B:1001 , HOH B:1004
BINDING SITE FOR RESIDUE RBF B 502
08
AC8
SOFTWARE
ILE B:118 , LEU B:119 , HIS B:142 , TRP C:27 , GLY C:61 , SER C:62 , TRP C:63 , GLU C:64 , VAL C:86 , LEU C:87 , ILE C:88 , HIS C:94 , PO4 C:1003 , HOH C:1005 , HOH C:1024
BINDING SITE FOR RESIDUE RBF C 503
09
AC9
SOFTWARE
ILE C:118 , LEU C:119 , HIS C:142 , TRP C:146 , TRP D:27 , GLY D:61 , SER D:62 , TRP D:63 , GLU D:64 , VAL D:86 , LEU D:87 , ILE D:88 , HIS D:94 , ILE D:98 , PO4 D:1005 , HOH D:1007
BINDING SITE FOR RESIDUE RBF D 504
10
BC1
SOFTWARE
ILE D:118 , LEU D:119 , HIS D:142 , TRP D:146 , TRP E:27 , GLY E:61 , SER E:62 , TRP E:63 , GLU E:64 , VAL E:86 , LEU E:87 , ILE E:88 , HIS E:94 , PO4 E:1002 , HOH E:1005
BINDING SITE FOR RESIDUE RBF E 505
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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Sorry, no Info available
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Exons
(0, 0)
Info
All 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1kyva_ (A:)
1b: SCOP_d1kyvb_ (B:)
1c: SCOP_d1kyvc_ (C:)
1d: SCOP_d1kyvd_ (D:)
1e: SCOP_d1kyve_ (E:)
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(
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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
:
Lumazine synthase
(19)
Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]
(7)
1a
d1kyva_
A:
1b
d1kyvb_
B:
1c
d1kyvc_
C:
1d
d1kyvd_
D:
1e
d1kyve_
E:
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1kyvE00 (E:7-158)
1b: CATH_1kyvA00 (A:12-158)
1c: CATH_1kyvB00 (B:12-158)
1d: CATH_1kyvD00 (D:12-158)
1e: CATH_1kyvC00 (C:11-159)
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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)
Fission yeast (Schizosaccharomyces pombe)
(10)
1a
1kyvE00
E:7-158
1b
1kyvA00
A:12-158
1c
1kyvB00
B:12-158
1d
1kyvD00
D:12-158
1e
1kyvC00
C:11-159
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_DMRL_synthase_1kyvE01 (E:15-157)
1b: PFAM_DMRL_synthase_1kyvE02 (E:15-157)
1c: PFAM_DMRL_synthase_1kyvE03 (E:15-157)
1d: PFAM_DMRL_synthase_1kyvE04 (E:15-157)
1e: PFAM_DMRL_synthase_1kyvE05 (E:15-157)
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)
Clan
:
no clan defined [family: DMRL_synthase]
(19)
Family
:
DMRL_synthase
(19)
Schizosaccharomyces pombe (strain ATCC 38366 / 972) (Fission yeast)
(7)
1a
DMRL_synthase-1kyvE01
E:15-157
1b
DMRL_synthase-1kyvE02
E:15-157
1c
DMRL_synthase-1kyvE03
E:15-157
1d
DMRL_synthase-1kyvE04
E:15-157
1e
DMRL_synthase-1kyvE05
E:15-157
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (127 KB)
Header - Asym.Unit
Biol.Unit 1 (121 KB)
Header - Biol.Unit 1
Biol.Unit 2 (239 KB)
Header - Biol.Unit 2
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