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1NQW
Biol. Unit 1
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Asym.Unit (136 KB)
Biol.Unit 1, α-C (1.5 MB)
Biol.Unit 1 (1.5 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS IN COMPLEX WITH INHIBITOR: 5-(6-D-RIBITYLAMINO-2,4(1H,3H) PYRIMIDINEDIONE-5-YL)-1-PENTYL-PHOSPHONIC ACID
Authors
:
X. Zhang, W. Meining, M. Cushman, I. Haase, M. Fischer, A. Bacher, R. Lad
Date
:
23 Jan 03 (Deposition) - 23 Jan 04 (Release) - 16 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (12x)
Keywords
:
Lumazine Synthase, Aquifex Aeolicus, Inhibitor Complex, Vitamin Biosynthesis, Catalytic Mechanism, Transferase
(Keyword Search:
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Reference
:
X. Zhang, W. Meining, M. Cushman, I. Haase, M. Fischer, A. Bacher, R. Ladenstein
A Structure-Based Model Of The Reaction Catalyzed By Lumazine Synthase From Aquifex Aeolicus.
J. Mol. Biol. V. 328 167 2003
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Hetero Components
(1, 60)
Info
All Hetero Components
1a: 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRI... (5YLa)
1b: 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRI... (5YLb)
1c: 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRI... (5YLc)
1d: 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRI... (5YLd)
1e: 5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRI... (5YLe)
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No.
Name
Count
Type
Full Name
1
5YL
60
Ligand/Ion
5-(6-D-RIBITYLAMINO-2,4(1H,3H)PYRIMIDINEDIONE-5-YL)PENTYL-1-PHOSPHONIC ACID
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE A:22 , ASN A:23 , GLY A:55 , SER A:56 , TRP A:57 , GLU A:58 , VAL A:80 , LEU A:81 , ILE A:82 , GLY A:84 , ALA A:85 , THR A:86 , HOH A:1301 , HOH A:1303 , HOH A:1339 , HOH A:1341 , HOH A:1349 , HOH A:1358 , HOH A:1376 , THR B:112 , PHE B:113 , ARG B:127 , LYS B:135 , GLU B:138
BINDING SITE FOR RESIDUE 5YL A 1201
2
AC2
SOFTWARE
PHE B:22 , ASN B:23 , GLY B:55 , SER B:56 , TRP B:57 , GLU B:58 , VAL B:80 , LEU B:81 , ILE B:82 , GLY B:84 , ALA B:85 , THR B:86 , HOH B:2301 , HOH B:2303 , HOH B:2319 , HOH B:2339 , HOH B:2349 , HOH B:2358 , HOH B:2376 , THR C:112 , PHE C:113 , ARG C:127 , LYS C:135 , GLU C:138 , HOH C:2341
BINDING SITE FOR RESIDUE 5YL B 2201
3
AC3
SOFTWARE
PHE C:22 , ASN C:23 , GLY C:55 , SER C:56 , TRP C:57 , GLU C:58 , VAL C:80 , LEU C:81 , ILE C:82 , GLY C:84 , ALA C:85 , THR C:86 , HOH C:3301 , HOH C:3303 , HOH C:3339 , HOH C:3341 , HOH C:3349 , HOH C:3358 , HOH C:3376 , THR D:112 , PHE D:113 , ARG D:127 , LYS D:135 , GLU D:138
BINDING SITE FOR RESIDUE 5YL C 3201
4
AC4
SOFTWARE
PHE D:22 , ASN D:23 , GLY D:55 , SER D:56 , TRP D:57 , GLU D:58 , VAL D:80 , LEU D:81 , ILE D:82 , GLY D:84 , ALA D:85 , THR D:86 , HOH D:4301 , HOH D:4303 , HOH D:4319 , HOH D:4339 , HOH D:4349 , HOH D:4358 , HOH D:4376 , THR E:112 , PHE E:113 , ARG E:127 , LYS E:135 , GLU E:138 , HOH E:4341
BINDING SITE FOR RESIDUE 5YL D 4201
5
AC5
SOFTWARE
THR A:112 , PHE A:113 , ARG A:127 , LYS A:135 , GLU A:138 , HOH A:5319 , PHE E:22 , ASN E:23 , GLY E:55 , SER E:56 , TRP E:57 , GLU E:58 , VAL E:80 , LEU E:81 , ILE E:82 , GLY E:84 , ALA E:85 , THR E:86 , HOH E:5301 , HOH E:5303 , HOH E:5339 , HOH E:5341 , HOH E:5349 , HOH E:5358 , HOH E:5376
BINDING SITE FOR RESIDUE 5YL E 5201
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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
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d1nqwa_ (A:)
1b: SCOP_d1nqwb_ (B:)
1c: SCOP_d1nqwc_ (C:)
1d: SCOP_d1nqwd_ (D:)
1e: SCOP_d1nqwe_ (E:)
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Protein Domains
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(
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Organisms
(
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(
)
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)
Aquifex aeolicus [TaxId: 63363]
(5)
1a
d1nqwa_
A:
1b
d1nqwb_
B:
1c
d1nqwc_
C:
1d
d1nqwd_
D:
1e
d1nqwe_
E:
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1nqwA00 (A:1-154)
1b: CATH_1nqwB00 (B:1-154)
1c: CATH_1nqwC00 (C:1-154)
1d: CATH_1nqwD00 (D:1-154)
1e: CATH_1nqwE00 (E:1-154)
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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)
Aquifex aeolicus. Organism_taxid: 63363.
(5)
1a
1nqwA00
A:1-154
1b
1nqwB00
B:1-154
1c
1nqwC00
C:1-154
1d
1nqwD00
D:1-154
1e
1nqwE00
E:1-154
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Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_DMRL_synthase_1nqwE01 (E:10-153)
1b: PFAM_DMRL_synthase_1nqwE02 (E:10-153)
1c: PFAM_DMRL_synthase_1nqwE03 (E:10-153)
1d: PFAM_DMRL_synthase_1nqwE04 (E:10-153)
1e: PFAM_DMRL_synthase_1nqwE05 (E:10-153)
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Clan
:
no clan defined [family: DMRL_synthase]
(19)
Family
:
DMRL_synthase
(19)
Aquifex aeolicus
(4)
1a
DMRL_synthase-1nqwE01
E:10-153
1b
DMRL_synthase-1nqwE02
E:10-153
1c
DMRL_synthase-1nqwE03
E:10-153
1d
DMRL_synthase-1nqwE04
E:10-153
1e
DMRL_synthase-1nqwE05
E:10-153
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