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3IEM
Asym. Unit
Info
Asym.Unit (302 KB)
Biol.Unit 1 (81 KB)
Biol.Unit 2 (78 KB)
Biol.Unit 3 (76 KB)
Biol.Unit 4 (77 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TTHA0252 FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH RNA ANALOG
Authors
:
H. Ishikawa, N. Nakagawa, S. Kuramitus, S. Yokoyama, R. Masui
Date
:
23 Jul 09 (Deposition) - 28 Jul 10 (Release) - 28 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,G,J,L,N (1x)
Biol. Unit 2: B,H,K (1x)
Biol. Unit 3: C,O,P (1x)
Biol. Unit 4: D,I,M (1x)
Keywords
:
Metallo Beta Lactamase Fold, Endonuclease, Hydrolase, Metal-Binding, Nuclease, Rna-Binding, Rrna Processing, Hydrolase-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ishikawa, N. Nakagawa, S. Kuramitsu, R. Masui
Crystal Structure Of Ttha0252 From Thermus Thermophilus Hb8 Complexed With Rna Analog
To Be Published
[
close entry info
]
Hetero Components
(4, 103)
Info
All Hetero Components
1a: CITRATE ANION (FLCa)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2ak: SULFATE ION (SO4ak)
2al: SULFATE ION (SO4al)
2am: SULFATE ION (SO4am)
2an: SULFATE ION (SO4an)
2ao: SULFATE ION (SO4ao)
2ap: SULFATE ION (SO4ap)
2aq: SULFATE ION (SO4aq)
2ar: SULFATE ION (SO4ar)
2as: SULFATE ION (SO4as)
2at: SULFATE ION (SO4at)
2au: SULFATE ION (SO4au)
2av: SULFATE ION (SO4av)
2aw: SULFATE ION (SO4aw)
2ax: SULFATE ION (SO4ax)
2ay: SULFATE ION (SO4ay)
2az: SULFATE ION (SO4az)
2b: SULFATE ION (SO4b)
2ba: SULFATE ION (SO4ba)
2bb: SULFATE ION (SO4bb)
2bc: SULFATE ION (SO4bc)
2bd: SULFATE ION (SO4bd)
2be: SULFATE ION (SO4be)
2bf: SULFATE ION (SO4bf)
2bg: SULFATE ION (SO4bg)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
3a: URIDINE-5'-PHOSPHOROTHIOATE (SSUa)
3aa: URIDINE-5'-PHOSPHOROTHIOATE (SSUaa)
3ab: URIDINE-5'-PHOSPHOROTHIOATE (SSUab)
3ac: URIDINE-5'-PHOSPHOROTHIOATE (SSUac)
3ad: URIDINE-5'-PHOSPHOROTHIOATE (SSUad)
3ae: URIDINE-5'-PHOSPHOROTHIOATE (SSUae)
3af: URIDINE-5'-PHOSPHOROTHIOATE (SSUaf)
3ag: URIDINE-5'-PHOSPHOROTHIOATE (SSUag)
3ah: URIDINE-5'-PHOSPHOROTHIOATE (SSUah)
3ai: URIDINE-5'-PHOSPHOROTHIOATE (SSUai)
3b: URIDINE-5'-PHOSPHOROTHIOATE (SSUb)
3c: URIDINE-5'-PHOSPHOROTHIOATE (SSUc)
3d: URIDINE-5'-PHOSPHOROTHIOATE (SSUd)
3e: URIDINE-5'-PHOSPHOROTHIOATE (SSUe)
3f: URIDINE-5'-PHOSPHOROTHIOATE (SSUf)
3g: URIDINE-5'-PHOSPHOROTHIOATE (SSUg)
3h: URIDINE-5'-PHOSPHOROTHIOATE (SSUh)
3i: URIDINE-5'-PHOSPHOROTHIOATE (SSUi)
3j: URIDINE-5'-PHOSPHOROTHIOATE (SSUj)
3k: URIDINE-5'-PHOSPHOROTHIOATE (SSUk)
3l: URIDINE-5'-PHOSPHOROTHIOATE (SSUl)
3m: URIDINE-5'-PHOSPHOROTHIOATE (SSUm)
3n: URIDINE-5'-PHOSPHOROTHIOATE (SSUn)
3o: URIDINE-5'-PHOSPHOROTHIOATE (SSUo)
3p: URIDINE-5'-PHOSPHOROTHIOATE (SSUp)
3q: URIDINE-5'-PHOSPHOROTHIOATE (SSUq)
3r: URIDINE-5'-PHOSPHOROTHIOATE (SSUr)
3s: URIDINE-5'-PHOSPHOROTHIOATE (SSUs)
3t: URIDINE-5'-PHOSPHOROTHIOATE (SSUt)
3u: URIDINE-5'-PHOSPHOROTHIOATE (SSUu)
3v: URIDINE-5'-PHOSPHOROTHIOATE (SSUv)
3w: URIDINE-5'-PHOSPHOROTHIOATE (SSUw)
3x: URIDINE-5'-PHOSPHOROTHIOATE (SSUx)
3y: URIDINE-5'-PHOSPHOROTHIOATE (SSUy)
3z: URIDINE-5'-PHOSPHOROTHIOATE (SSUz)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FLC
1
Ligand/Ion
CITRATE ANION
2
SO4
59
Ligand/Ion
SULFATE ION
3
SSU
35
Mod. Nucleotide
URIDINE-5'-PHOSPHOROTHIOATE
4
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(67, 67)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
56: GC2 (SOFTWARE)
57: GC3 (SOFTWARE)
58: GC4 (SOFTWARE)
59: GC5 (SOFTWARE)
60: GC6 (SOFTWARE)
61: GC7 (SOFTWARE)
62: GC8 (SOFTWARE)
63: GC9 (SOFTWARE)
64: HC1 (SOFTWARE)
65: HC2 (SOFTWARE)
66: HC3 (SOFTWARE)
67: HC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:241 , HOH A:521 , SER B:330 , ASP B:331
BINDING SITE FOR RESIDUE SO4 A 432
02
AC2
SOFTWARE
ARG A:192 , ARG A:195 , GLY A:375 , HOH A:491 , HOH A:529
BINDING SITE FOR RESIDUE SO4 A 433
03
AC3
SOFTWARE
LYS A:298 , HIS A:323 , LYS A:326 , HIS A:327
BINDING SITE FOR RESIDUE SO4 A 434
04
AC4
SOFTWARE
ARG A:198 , GLU A:199 , ARG A:202
BINDING SITE FOR RESIDUE SO4 A 435
05
AC5
SOFTWARE
ARG A:77 , GLU A:113 , HIS A:117
BINDING SITE FOR RESIDUE SO4 A 436
06
AC6
SOFTWARE
PRO A:172 , ASP A:173 , SER A:269 , GLU A:270 , HOH A:490 , HOH A:500
BINDING SITE FOR RESIDUE SO4 A 437
07
AC7
SOFTWARE
ARG A:24 , LEU A:129 , GLY A:130 , HOH A:507
BINDING SITE FOR RESIDUE SO4 A 438
08
AC8
SOFTWARE
PRO A:304 , ASP A:331 , ARG A:333
BINDING SITE FOR RESIDUE SO4 A 439
09
AC9
SOFTWARE
ARG A:195 , GLU A:199 , LYS D:326 , HIS D:327 , SER D:330
BINDING SITE FOR RESIDUE SO4 A 440
10
BC1
SOFTWARE
HIS A:61 , LEU A:142 , PHE A:223 , VAL A:225 , GLU A:226 , ARG A:227 , SSU G:4 , HOH G:97
BINDING SITE FOR RESIDUE SO4 A 441
11
BC2
SOFTWARE
ARG A:202 , HIS A:238 , HIS A:240 , ARG A:241 , PRO B:366 , ARG B:368
BINDING SITE FOR RESIDUE SO4 A 442
12
BC3
SOFTWARE
PRO A:252 , MET A:253 , ARG A:256 , SSU G:6
BINDING SITE FOR RESIDUE SO4 A 443
13
BC4
SOFTWARE
HIS A:293 , THR A:294 , GLU A:295 , SSU G:6
BINDING SITE FOR RESIDUE SO4 A 444
14
BC5
SOFTWARE
ARG A:368
BINDING SITE FOR RESIDUE SO4 A 445
15
BC6
SOFTWARE
TYR A:248 , GLU A:289 , ALA A:296 , TYR B:248 , GLU B:289 , HOH B:496
BINDING SITE FOR RESIDUE SO4 A 446
16
BC7
SOFTWARE
MET A:1 , ARG A:2 , HOH A:498
BINDING SITE FOR RESIDUE SO4 A 447
17
BC8
SOFTWARE
ASP A:63 , HIS A:64 , ASP A:162 , HIS A:400 , ZN A:449 , SSU G:3
BINDING SITE FOR RESIDUE ZN A 448
18
BC9
SOFTWARE
HIS A:59 , HIS A:61 , HIS A:141 , ASP A:162 , ZN A:448 , SSU G:3
BINDING SITE FOR RESIDUE ZN A 449
19
CC1
SOFTWARE
PRO B:243 , ARG B:244
BINDING SITE FOR RESIDUE SO4 B 432
20
CC2
SOFTWARE
ARG B:24
BINDING SITE FOR RESIDUE SO4 B 433
21
CC3
SOFTWARE
ARG B:84 , ARG B:263
BINDING SITE FOR RESIDUE SO4 B 434
22
CC4
SOFTWARE
ARG B:354 , SO4 B:448
BINDING SITE FOR RESIDUE SO4 B 435
23
CC5
SOFTWARE
TYR B:189 , ARG B:227 , GLY B:340 , TYR B:341 , SER B:378 , GLY B:379 , SSU K:1
BINDING SITE FOR RESIDUE SO4 B 436
24
CC6
SOFTWARE
LEU B:387 , LEU B:412
BINDING SITE FOR RESIDUE SO4 B 437
25
CC7
SOFTWARE
ARG B:24 , LEU B:129 , GLY B:130
BINDING SITE FOR RESIDUE SO4 B 438
26
CC8
SOFTWARE
ARG B:195 , GLY B:375 , GLY B:376 , HOH B:500
BINDING SITE FOR RESIDUE SO4 B 439
27
CC9
SOFTWARE
HIS B:372 , THR B:373 , SO4 B:441
BINDING SITE FOR RESIDUE SO4 B 440
28
DC1
SOFTWARE
ILE B:352 , ARG B:354 , VAL B:371 , SO4 B:440 , SO4 B:448
BINDING SITE FOR RESIDUE SO4 B 441
29
DC2
SOFTWARE
PRO B:172 , ASP B:173 , SER B:269 , GLU B:270
BINDING SITE FOR RESIDUE SO4 B 442
30
DC3
SOFTWARE
SER B:370 , HIS B:372 , SO4 B:448
BINDING SITE FOR RESIDUE SO4 B 443
31
DC4
SOFTWARE
ARG B:320 , HOH B:517 , HOH K:524
BINDING SITE FOR RESIDUE SO4 B 444
32
DC5
SOFTWARE
HIS B:293 , THR B:294 , GLU B:295 , HOH B:517 , SSU L:2
BINDING SITE FOR RESIDUE SO4 B 445
33
DC6
SOFTWARE
ARG B:359 , LEU B:361 , HOH B:464
BINDING SITE FOR RESIDUE SO4 B 446
34
DC7
SOFTWARE
ARG A:244 , LYS B:298
BINDING SITE FOR RESIDUE SO4 B 447
35
DC8
SOFTWARE
ARG B:354 , ALA B:369 , SER B:370 , VAL B:371 , SO4 B:435 , SO4 B:441 , SO4 B:443
BINDING SITE FOR RESIDUE SO4 B 448
36
DC9
SOFTWARE
ARG A:244 , HIS B:323 , LYS B:326 , HIS B:327
BINDING SITE FOR RESIDUE SO4 B 449
37
EC1
SOFTWARE
LEU A:407 , GLY A:410 , LYS A:411 , LEU B:407 , GLY B:410 , LYS B:411
BINDING SITE FOR RESIDUE FLC B 450
38
EC2
SOFTWARE
ASP B:63 , HIS B:64 , ASP B:162 , HIS B:400 , ZN B:452 , SSU K:1
BINDING SITE FOR RESIDUE ZN B 451
39
EC3
SOFTWARE
HIS B:59 , HIS B:61 , HIS B:141 , ASP B:162 , ZN B:451 , SSU K:1
BINDING SITE FOR RESIDUE ZN B 452
40
EC4
SOFTWARE
VAL C:291 , GLU C:292 , HIS C:293
BINDING SITE FOR RESIDUE SO4 C 432
41
EC5
SOFTWARE
ARG C:354
BINDING SITE FOR RESIDUE SO4 C 433
42
EC6
SOFTWARE
ARG C:24 , LEU C:129 , GLY C:130
BINDING SITE FOR RESIDUE SO4 C 434
43
EC7
SOFTWARE
ARG C:84 , LEU C:88 , ARG C:263 , ARG C:266
BINDING SITE FOR RESIDUE SO4 C 435
44
EC8
SOFTWARE
ARG C:155
BINDING SITE FOR RESIDUE SO4 C 436
45
EC9
SOFTWARE
ARG C:10 , ARG C:424
BINDING SITE FOR RESIDUE SO4 C 437
46
FC1
SOFTWARE
ARG A:73 , ARG C:424
BINDING SITE FOR RESIDUE SO4 C 438
47
FC2
SOFTWARE
LEU C:171 , PRO C:172 , ASP C:173 , SER C:269 , GLU C:270
BINDING SITE FOR RESIDUE SO4 C 439
48
FC3
SOFTWARE
GLU C:153 , HOH C:461
BINDING SITE FOR RESIDUE SO4 C 440
49
FC4
SOFTWARE
HIS C:42 , PRO C:104 , PHE C:105
BINDING SITE FOR RESIDUE SO4 C 441
50
FC5
SOFTWARE
TYR C:189 , ARG C:227 , GLY C:340 , TYR C:341 , SER C:378 , GLY C:379 , SSU P:1
BINDING SITE FOR RESIDUE SO4 C 442
51
FC6
SOFTWARE
ARG A:73 , ARG C:424
BINDING SITE FOR RESIDUE SO4 C 443
52
FC7
SOFTWARE
ASP C:63 , HIS C:64 , ASP C:162 , HIS C:400 , ZN C:445
BINDING SITE FOR RESIDUE ZN C 444
53
FC8
SOFTWARE
HIS C:59 , HIS C:61 , HIS C:141 , ASP C:162 , ZN C:444
BINDING SITE FOR RESIDUE ZN C 445
54
FC9
SOFTWARE
ARG D:263
BINDING SITE FOR RESIDUE SO4 D 432
55
GC1
SOFTWARE
PRO D:366 , ARG D:368
BINDING SITE FOR RESIDUE SO4 D 433
56
GC2
SOFTWARE
ARG D:24 , ARG D:128 , LEU D:129 , GLY D:130
BINDING SITE FOR RESIDUE SO4 D 435
57
GC3
SOFTWARE
ARG A:84 , PRO A:120 , GLU A:122 , ARG A:266 , GLU D:270 , HOH D:446
BINDING SITE FOR RESIDUE SO4 D 436
58
GC4
SOFTWARE
ARG D:155
BINDING SITE FOR RESIDUE SO4 D 437
59
GC5
SOFTWARE
PRO D:172 , ASP D:173 , SER D:269 , GLU D:270 , HOH D:467
BINDING SITE FOR RESIDUE SO4 D 438
60
GC6
SOFTWARE
LYS D:298 , HIS D:323 , LYS D:326 , HIS D:327
BINDING SITE FOR RESIDUE SO4 D 439
61
GC7
SOFTWARE
HIS D:42 , PHE D:105 , HOH D:461
BINDING SITE FOR RESIDUE SO4 D 440
62
GC8
SOFTWARE
MET D:1 , ARG D:2
BINDING SITE FOR RESIDUE SO4 D 441
63
GC9
SOFTWARE
ARG D:77 , GLU D:113 , HIS D:117
BINDING SITE FOR RESIDUE SO4 D 442
64
HC1
SOFTWARE
ASP D:63 , HIS D:64 , ASP D:162 , HIS D:400 , ZN D:444 , SSU I:3
BINDING SITE FOR RESIDUE ZN D 443
65
HC2
SOFTWARE
HIS D:59 , HIS D:61 , HIS D:141 , ASP D:162 , ZN D:443 , SSU I:3
BINDING SITE FOR RESIDUE ZN D 444
66
HC3
SOFTWARE
SSU J:3
BINDING SITE FOR RESIDUE SO4 J 40
67
HC4
SOFTWARE
SSU K:3 , HOH K:227 , HOH K:524
BINDING SITE FOR RESIDUE SO4 K 36
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3iema_ (A:)
1b: SCOP_d3iemc_ (C:)
1c: SCOP_d3iemd_ (D:)
1d: SCOP_d3iemb_ (B:)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-hydrolase/oxidoreductase
(184)
Superfamily
:
Metallo-hydrolase/oxidoreductase
(184)
Family
:
beta-CASP RNA-metabolising hydrolases
(13)
Protein domain
:
Putative RNA-degradation protein TTHA0252
(9)
Thermus thermophilus [TaxId: 274]
(9)
1a
d3iema_
A:
1b
d3iemc_
C:
1c
d3iemd_
D:
1d
d3iemb_
B:
[
close SCOP info
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (302 KB)
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Biol.Unit 1 (81 KB)
Header - Biol.Unit 1
Biol.Unit 2 (78 KB)
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Biol.Unit 3 (76 KB)
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