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4KQ6
Biol. Unit 2
Info
Asym.Unit (276 KB)
Biol.Unit 1 (139 KB)
Biol.Unit 2 (134 KB)
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(1)
Title
:
PRODUCT COMPLEX OF LUMAZINE SYNTHASE FROM CANDIDA GLABRATA
Authors
:
M. Shankar, S. M. Wilbanks, Y. Nakatani, B. C. Monk, J. D. A. Tyndall
Date
:
14 May 13 (Deposition) - 29 May 13 (Release) - 28 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.24
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
:
Lumazine Synthase, Riboflavin Biosynthesis, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Shankar, S. M. Wilbanks, Y. Nakatani, B. C. Monk, J. D. Tyndall
Catalysis Product Captured In Lumazine Synthase From The Fungal Pathogen Candida Glabrata.
Acta Crystallogr. , Sect. D V. 69 1580 2013
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Hetero Components
(3, 17)
Info
All Hetero Components
1a: 1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-... (DLZa)
1b: 1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-... (DLZb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
3p: SULFATE ION (SO4p)
3q: SULFATE ION (SO4q)
3r: SULFATE ION (SO4r)
3s: SULFATE ION (SO4s)
3t: SULFATE ION (SO4t)
3u: SULFATE ION (SO4u)
3v: SULFATE ION (SO4v)
3w: SULFATE ION (SO4w)
3x: SULFATE ION (SO4x)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DLZ
1
Ligand/Ion
1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-3,4-DIHYDROPTERIDIN-8(2H)-YL)-D-RIBITOL
2
GOL
3
Ligand/Ion
GLYCEROL
3
SO4
13
Ligand/Ion
SULFATE ION
[
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Sites
(17, 17)
Info
All Sites
01: BC6 (SOFTWARE)
02: BC7 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
14: DC1 (SOFTWARE)
15: DC2 (SOFTWARE)
16: DC3 (SOFTWARE)
17: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC6
SOFTWARE
TRP F:27 , ASN F:28 , ARG F:29 , HOH F:348
BINDING SITE FOR RESIDUE SO4 F 201
02
BC7
SOFTWARE
MET F:146 , HIS F:147
BINDING SITE FOR RESIDUE SO4 F 202
03
BC8
SOFTWARE
GLY F:94 , SER F:95 , THR F:96 , HIS F:98 , HOH F:314 , HOH F:357 , HOH F:361 , ARG G:137
BINDING SITE FOR RESIDUE SO4 F 203
04
BC9
SOFTWARE
TRP G:27 , ASN G:28 , ARG G:29
BINDING SITE FOR RESIDUE SO4 G 201
05
CC1
SOFTWARE
THR G:145 , MET G:146 , HIS G:147
BINDING SITE FOR RESIDUE SO4 G 202
06
CC2
SOFTWARE
GLY G:94 , SER G:95 , THR G:96 , HIS G:98 , ARG H:137
BINDING SITE FOR RESIDUE SO4 G 203
07
CC3
SOFTWARE
GLY G:60 , SER G:61 , PHE G:62 , GLU G:63 , ILE H:122 , PHE H:123
BINDING SITE FOR RESIDUE GOL G 204
08
CC4
SOFTWARE
GLY H:94 , SER H:95 , THR H:96 , HIS H:98 , HOH H:330 , HOH H:343 , ARG I:137
BINDING SITE FOR RESIDUE SO4 H 201
09
CC5
SOFTWARE
TRP H:27 , ASN H:28 , ARG H:29 , HOH H:351
BINDING SITE FOR RESIDUE SO4 H 202
10
CC6
SOFTWARE
MET I:146 , HIS I:147
BINDING SITE FOR RESIDUE SO4 I 201
11
CC7
SOFTWARE
GLY I:94 , SER I:95 , THR I:96 , DLZ I:204 , HOH I:346 , ARG J:137
BINDING SITE FOR RESIDUE SO4 I 202
12
CC8
SOFTWARE
GLY H:60 , GLU H:63 , HOH H:352 , ILE I:122 , PHE I:123 , HOH I:357
BINDING SITE FOR RESIDUE GOL I 203
13
CC9
SOFTWARE
TRP I:27 , GLY I:60 , SER I:61 , PHE I:62 , GLU I:63 , VAL I:90 , LEU I:91 , HIS I:98 , SO4 I:202 , ILE J:122 , PHE J:123 , HOH J:334
BINDING SITE FOR RESIDUE DLZ I 204
14
DC1
SOFTWARE
TRP J:27 , ASN J:28 , ARG J:29
BINDING SITE FOR RESIDUE SO4 J 201
15
DC2
SOFTWARE
ARG F:137 , GLY J:94 , SER J:95 , THR J:96 , HOH J:374
BINDING SITE FOR RESIDUE SO4 J 202
16
DC3
SOFTWARE
LYS J:17 , ASN J:52
BINDING SITE FOR RESIDUE SO4 J 203
17
DC4
SOFTWARE
ILE F:122 , PHE F:123 , GLU J:63 , HOH J:309
BINDING SITE FOR RESIDUE GOL J 204
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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Sorry, no Info available
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Exons
(0, 0)
Info
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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, 10)
Info
All SCOP Domains
1a: SCOP_d4kq6a_ (A:)
1b: SCOP_d4kq6b_ (B:)
1c: SCOP_d4kq6c_ (C:)
1d: SCOP_d4kq6d_ (D:)
1e: SCOP_d4kq6e_ (E:)
1f: SCOP_d4kq6f_ (F:)
1g: SCOP_d4kq6g_ (G:)
1h: SCOP_d4kq6h_ (H:)
1i: SCOP_d4kq6i_ (I:)
1j: SCOP_d4kq6j_ (J:)
View:
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Classes
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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)
Candida glabrata [TaxId: 284593]
(1)
1a
d4kq6a_
A:
1b
d4kq6b_
B:
1c
d4kq6c_
C:
1d
d4kq6d_
D:
1e
d4kq6e_
E:
1f
d4kq6f_
F:
1g
d4kq6g_
G:
1h
d4kq6h_
H:
1i
d4kq6i_
I:
1j
d4kq6j_
J:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Sidechain
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
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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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (276 KB)
Header - Asym.Unit
Biol.Unit 1 (139 KB)
Header - Biol.Unit 1
Biol.Unit 2 (134 KB)
Header - Biol.Unit 2
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