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1T9H
Asym. Unit
Info
Asym.Unit (115 KB)
Biol.Unit 1 (108 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF YLOQ, A CIRCULARLY PERMUTED GTPASE.
Authors
:
V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Cladiere, A. A. Antson, M. N. Isupov, S. J. Seror, A. J. Wilkinson
Date
:
17 May 04 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
N-Terminal Beta-Barrel Domain With Oligonucleotide Binding Fold, Central Gtp Binding Domain, C-Terminal Zinc-Binding Domain, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Levdikov, E. V. Blagova, J. A. Brannigan, L. Cladiere, A. A. Antson, M. N. Isupov, S. J. Seror, A. J. Wilkinson
The Crystal Structure Of Yloq, A Circularly Permuted Gtpase Essential For Bacillus Subtilis Viability.
J. Mol. Biol. V. 340 767 2004
(for further references see the
PDB file header
)
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: URANYL (VI) ION (IUMa)
3b: URANYL (VI) ION (IUMb)
3c: URANYL (VI) ION (IUMc)
3d: URANYL (VI) ION (IUMd)
3e: URANYL (VI) ION (IUMe)
3f: URANYL (VI) ION (IUMf)
3g: URANYL (VI) ION (IUMg)
3h: URANYL (VI) ION (IUMh)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
CA
4
Ligand/Ion
CALCIUM ION
3
IUM
8
Ligand/Ion
URANYL (VI) ION
4
ZN
1
Ligand/Ion
ZINC ION
[
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]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:-2 , HIS A:-4 , HIS A:-3 , HIS A:-1 , ASN A:54 , IUM A:407 , ACT A:417 , HOH A:424 , HOH A:436 , HOH A:479
BINDING SITE FOR RESIDUE IUM A 401
02
AC2
SOFTWARE
HIS A:-4 , GLU A:105 , PRO A:111 , PRO A:243 , ARG A:246 , IUM A:408 , ACT A:416 , HOH A:419 , HOH A:420 , HOH A:465
BINDING SITE FOR RESIDUE IUM A 402
03
AC3
SOFTWARE
ARG A:246 , IUM A:404 , IUM A:406 , IUM A:408 , ACT A:416 , ACT A:418 , HOH A:419 , HOH A:422 , HOH A:440 , HOH A:463
BINDING SITE FOR RESIDUE IUM A 403
04
AC4
SOFTWARE
ARG A:30 , GLU A:57 , IUM A:403 , ACT A:418 , HOH A:422 , HOH A:425 , HOH A:458
BINDING SITE FOR RESIDUE IUM A 404
05
AC5
SOFTWARE
GLU A:53 , LYS A:56 , GLU A:57 , TYR A:59 , HOH A:425
BINDING SITE FOR RESIDUE IUM A 405
06
AC6
SOFTWARE
HIS A:-1 , GLU A:53 , LYS A:56 , IUM A:403 , IUM A:408 , ACT A:417 , HOH A:422 , HOH A:425 , HOH A:440 , HOH A:458 , HOH A:587
BINDING SITE FOR RESIDUE IUM A 406
07
AC7
SOFTWARE
ARG A:-6 , HIS A:-5 , HIS A:-4 , HIS A:-3 , ASN A:54 , ASP A:108 , IUM A:401 , HOH A:436 , HOH A:451 , HOH A:453 , HOH A:607
BINDING SITE FOR RESIDUE IUM A 407
08
AC8
SOFTWARE
HIS A:-4 , HIS A:-1 , ARG A:246 , IUM A:402 , IUM A:403 , IUM A:406 , ACT A:417 , HOH A:419 , HOH A:420 , HOH A:424 , HOH A:440 , HOH A:465
BINDING SITE FOR RESIDUE IUM A 408
09
AC9
SOFTWARE
CYS A:252 , CYS A:257 , HIS A:259 , CYS A:265
BINDING SITE FOR RESIDUE ZN A 411
10
BC1
SOFTWARE
ASP A:143 , TYR A:145 , HOH A:549
BINDING SITE FOR RESIDUE CA A 412
11
BC2
SOFTWARE
HIS A:-1 , GLU A:247
BINDING SITE FOR RESIDUE CA A 413
12
BC3
SOFTWARE
GLU A:210 , HOH A:658 , HOH A:663
BINDING SITE FOR RESIDUE CA A 414
13
BC4
SOFTWARE
GLU A:286 , HOH A:521 , HOH A:595
BINDING SITE FOR RESIDUE CA A 415
14
BC5
SOFTWARE
GLU A:105 , GLY A:141 , TYR A:142 , PRO A:243 , IUM A:402 , IUM A:403 , ACT A:418 , HOH A:419
BINDING SITE FOR RESIDUE ACT A 416
15
BC6
SOFTWARE
HIS A:-2 , GLU A:53 , ASN A:54 , IUM A:401 , IUM A:406 , IUM A:408 , HOH A:424 , HOH A:440 , HOH A:587
BINDING SITE FOR RESIDUE ACT A 417
16
BC7
SOFTWARE
PHE A:13 , GLU A:57 , GLY A:141 , IUM A:403 , IUM A:404 , ACT A:416 , HOH A:422
BINDING SITE FOR RESIDUE ACT A 418
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: G_CP (A:67-228)
2: ENGC_GTPASE (A:76-226)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
G_CP
PS51721
Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile.
RSGA_BACSU
67-228
1
A:67-228
2
ENGC_GTPASE
PS50936
EngC GTPase domain profile.
RSGA_BACSU
76-226
1
A:76-226
[
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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.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1t9ha1 (A:1-67)
2a: SCOP_d1t9ha2 (A:68-298)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Cold shock DNA-binding domain-like
(310)
Protein domain
:
Probable GTPase EngC (YjeQ), N-terminal domain
(2)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d1t9ha1
A:1-67
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
G proteins
(693)
Protein domain
:
Probable GTPase EngC (YjeQ), C-terminal domain
(2)
Bacillus subtilis [TaxId: 1423]
(1)
2a
d1t9ha2
A:68-298
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1t9hA02 (A:66-230)
2a: CATH_1t9hA03 (A:231-298)
3a: CATH_1t9hA01 (A:-7-65)
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)
(
)
Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Bacillus subtilis. Organism_taxid: 1423.
(11)
1a
1t9hA02
A:66-230
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase Protein R1; domain 1
(62)
Homologous Superfamily
:
Probable gtpase engc; domain 3
(3)
Bacillus subtilis. Organism_taxid: 1423.
(1)
2a
1t9hA03
A:231-298
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Bacillus subtilis. Organism_taxid: 1423.
(6)
3a
1t9hA01
A:-7-65
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_DUF258_1t9hA01 (A:130-289)
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Clans
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Organisms
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(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
DUF258
(4)
Bacillus subtilis
(1)
1a
DUF258-1t9hA01
A:130-289
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Asymmetric Unit 1
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