PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3IE1
Asym. Unit
Info
Asym.Unit (289 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (74 KB)
Biol.Unit 4 (75 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF H380A MUTANT TTHA0252 FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH RNA
Authors
:
H. Ishikawa, N. Nakagawa, S. Kuramitsu, S. Yokoyama, R. Masui, Riken S Genomics/Proteomics Initiative (Rsgi)
Date
:
22 Jul 09 (Deposition) - 04 Aug 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Metallo Beta Lactamase Fold, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Endonuclease, 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 H380A Mutant Ttha0252 From Thermus Thermophilus Hb8 Complexed With Rna
To Be Published
[
close entry info
]
Hetero Components
(3, 64)
Info
All Hetero Components
1a: CITRATE ANION (FLCa)
1b: CITRATE ANION (FLCb)
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)
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: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
3g: ZINC ION (ZNg)
3h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FLC
2
Ligand/Ion
CITRATE ANION
2
SO4
54
Ligand/Ion
SULFATE ION
3
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(64, 64)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:192 , ARG A:195 , GLY A:375 , GLY A:376 , HOH A:458
BINDING SITE FOR RESIDUE SO4 A 432
02
AC2
SOFTWARE
HIS A:238 , HIS A:240 , ARG A:241 , ARG B:368
BINDING SITE FOR RESIDUE SO4 A 433
03
AC3
SOFTWARE
ARG A:24 , ARG A:128 , LEU A:129 , GLY A:130
BINDING SITE FOR RESIDUE SO4 A 434
04
AC4
SOFTWARE
FLC A:450
BINDING SITE FOR RESIDUE SO4 A 435
05
AC5
SOFTWARE
ARG A:333
BINDING SITE FOR RESIDUE SO4 A 436
06
AC6
SOFTWARE
MET A:1 , ARG A:2
BINDING SITE FOR RESIDUE SO4 A 437
07
AC7
SOFTWARE
PRO A:172 , ASP A:173 , SER A:269 , GLU A:270
BINDING SITE FOR RESIDUE SO4 A 438
08
AC8
SOFTWARE
SER A:330 , PRO A:366 , ARG A:368
BINDING SITE FOR RESIDUE SO4 A 439
09
AC9
SOFTWARE
ARG A:359 , GLY A:362
BINDING SITE FOR RESIDUE SO4 A 440
10
BC1
SOFTWARE
ARG A:368
BINDING SITE FOR RESIDUE SO4 A 441
11
BC2
SOFTWARE
HIS A:293 , ARG B:284
BINDING SITE FOR RESIDUE SO4 A 442
12
BC3
SOFTWARE
LYS A:298 , ASN A:301 , HIS A:323 , LYS A:326 , HIS A:327
BINDING SITE FOR RESIDUE SO4 A 443
13
BC4
SOFTWARE
HIS A:293 , THR A:294 , GLU A:295 , GLY B:287
BINDING SITE FOR RESIDUE SO4 A 444
14
BC5
SOFTWARE
ASN A:281 , ARG A:284 , FLC A:450 , HOH A:461
BINDING SITE FOR RESIDUE SO4 A 445
15
BC6
SOFTWARE
ARG A:2 , GLU A:427 , GLY A:428
BINDING SITE FOR RESIDUE SO4 A 446
16
BC7
SOFTWARE
TYR A:189 , ARG A:227 , GLY A:340 , TYR A:341 , SER A:378 , GLY A:379
BINDING SITE FOR RESIDUE SO4 A 447
17
BC8
SOFTWARE
ARG A:284 , VAL A:290 , FLC A:450 , GLU B:292
BINDING SITE FOR RESIDUE SO4 A 448
18
BC9
SOFTWARE
ARG A:84 , LEU A:88 , ARG A:263
BINDING SITE FOR RESIDUE SO4 A 449
19
CC1
SOFTWARE
SER A:259 , PRO A:262 , ARG A:284 , SO4 A:435 , SO4 A:445 , SO4 A:448
BINDING SITE FOR RESIDUE FLC A 450
20
CC2
SOFTWARE
LEU A:407 , LYS A:411 , ALA A:414 , LEU B:407 , LYS B:411
BINDING SITE FOR RESIDUE FLC A 451
21
CC3
SOFTWARE
ASP A:63 , HIS A:64 , ASP A:162 , HIS A:400 , ZN A:453 , U E:1
BINDING SITE FOR RESIDUE ZN A 452
22
CC4
SOFTWARE
HIS A:59 , HIS A:61 , HIS A:141 , ASP A:162 , ZN A:452 , U E:1
BINDING SITE FOR RESIDUE ZN A 453
23
CC5
SOFTWARE
LEU B:387
BINDING SITE FOR RESIDUE SO4 B 432
24
CC6
SOFTWARE
ARG B:359 , GLY B:362
BINDING SITE FOR RESIDUE SO4 B 433
25
CC7
SOFTWARE
PRO B:243 , ARG B:244
BINDING SITE FOR RESIDUE SO4 B 434
26
CC8
SOFTWARE
ARG B:24
BINDING SITE FOR RESIDUE SO4 B 435
27
CC9
SOFTWARE
ARG B:284 , VAL B:290 , GLU B:292
BINDING SITE FOR RESIDUE SO4 B 436
28
DC1
SOFTWARE
LEU A:415 , ARG B:424
BINDING SITE FOR RESIDUE SO4 B 437
29
DC2
SOFTWARE
PRO A:243 , ARG A:244
BINDING SITE FOR RESIDUE SO4 B 438
30
DC3
SOFTWARE
ARG B:354
BINDING SITE FOR RESIDUE SO4 B 439
31
DC4
SOFTWARE
PRO B:172 , ASP B:173 , SER B:269 , GLU B:270
BINDING SITE FOR RESIDUE SO4 B 440
32
DC5
SOFTWARE
ARG B:24 , LEU B:129 , GLY B:130
BINDING SITE FOR RESIDUE SO4 B 441
33
DC6
SOFTWARE
GLU B:292 , HIS B:293 , THR B:294 , ARG B:320 , U F:4
BINDING SITE FOR RESIDUE SO4 B 442
34
DC7
SOFTWARE
ARG B:84 , ARG B:263
BINDING SITE FOR RESIDUE SO4 B 443
35
DC8
SOFTWARE
ARG A:244 , LYS B:298 , HIS B:323 , LYS B:326 , HIS B:327
BINDING SITE FOR RESIDUE SO4 B 444
36
DC9
SOFTWARE
ARG B:368
BINDING SITE FOR RESIDUE SO4 B 445
37
EC1
SOFTWARE
ARG B:2 , GLY B:426 , GLY B:428
BINDING SITE FOR RESIDUE SO4 B 446
38
EC2
SOFTWARE
ARG B:25 , PHE B:47 , ASP B:48 , GLU B:51
BINDING SITE FOR RESIDUE SO4 B 447
39
EC3
SOFTWARE
TYR B:189 , ARG B:227 , GLY B:340 , TYR B:341 , SER B:378 , GLY B:379
BINDING SITE FOR RESIDUE SO4 B 448
40
EC4
SOFTWARE
ASP B:63 , HIS B:64 , ASP B:162 , HIS B:400 , ZN B:450 , U F:1
BINDING SITE FOR RESIDUE ZN B 449
41
EC5
SOFTWARE
HIS B:59 , HIS B:61 , HIS B:141 , ASP B:162 , ZN B:449 , U F:1
BINDING SITE FOR RESIDUE ZN B 450
42
EC6
SOFTWARE
TYR C:189 , ARG C:227 , TYR C:341 , SER C:378 , GLY C:379 , ALA C:380
BINDING SITE FOR RESIDUE SO4 C 432
43
EC7
SOFTWARE
PRO C:172 , ASP C:173 , SER C:269 , GLU C:270
BINDING SITE FOR RESIDUE SO4 C 433
44
EC8
SOFTWARE
ARG C:25
BINDING SITE FOR RESIDUE SO4 C 434
45
EC9
SOFTWARE
ARG C:24 , LYS C:50
BINDING SITE FOR RESIDUE SO4 C 435
46
FC1
SOFTWARE
SER C:251 , PRO C:252 , MET C:253
BINDING SITE FOR RESIDUE SO4 C 436
47
FC2
SOFTWARE
ARG A:73 , ARG C:424
BINDING SITE FOR RESIDUE SO4 C 437
48
FC3
SOFTWARE
ARG C:84 , ARG C:263
BINDING SITE FOR RESIDUE SO4 C 438
49
FC4
SOFTWARE
ARG C:24 , ARG C:128 , LEU C:129 , GLY C:130
BINDING SITE FOR RESIDUE SO4 C 439
50
FC5
SOFTWARE
ARG C:2 , GLY C:428
BINDING SITE FOR RESIDUE SO4 C 440
51
FC6
SOFTWARE
ARG C:25 , PHE C:47 , ASP C:48
BINDING SITE FOR RESIDUE SO4 C 441
52
FC7
SOFTWARE
ASP C:63 , HIS C:64 , ASP C:162 , HIS C:400 , ZN C:443 , U G:1
BINDING SITE FOR RESIDUE ZN C 442
53
FC8
SOFTWARE
HIS C:59 , HIS C:61 , HIS C:141 , ASP C:162 , ZN C:442 , U G:1
BINDING SITE FOR RESIDUE ZN C 443
54
FC9
SOFTWARE
GLY D:35 , LYS D:36 , GLU D:38
BINDING SITE FOR RESIDUE SO4 D 432
55
GC1
SOFTWARE
ARG D:24
BINDING SITE FOR RESIDUE SO4 D 433
56
GC2
SOFTWARE
ARG D:84 , ARG D:263
BINDING SITE FOR RESIDUE SO4 D 434
57
GC3
SOFTWARE
ARG D:155
BINDING SITE FOR RESIDUE SO4 D 435
58
GC4
SOFTWARE
PRO D:172 , ASP D:173 , SER D:269 , GLU D:270
BINDING SITE FOR RESIDUE SO4 D 436
59
GC5
SOFTWARE
ARG D:2 , GLY D:428
BINDING SITE FOR RESIDUE SO4 D 437
60
GC6
SOFTWARE
ARG D:24 , ARG D:128 , LEU D:129 , GLY D:130
BINDING SITE FOR RESIDUE SO4 D 438
61
GC7
SOFTWARE
TYR D:189 , ARG D:227 , GLY D:340 , TYR D:341 , SER D:378 , GLY D:379
BINDING SITE FOR RESIDUE SO4 D 439
62
GC8
SOFTWARE
MET D:1
BINDING SITE FOR RESIDUE SO4 D 440
63
GC9
SOFTWARE
ASP D:63 , HIS D:64 , ASP D:162 , HIS D:400 , ZN D:442 , U H:1
BINDING SITE FOR RESIDUE ZN D 441
64
HC1
SOFTWARE
HIS D:59 , HIS D:61 , HIS D:141 , ASP D:162 , ZN D:441 , U H:1
BINDING SITE FOR RESIDUE ZN D 442
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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_d3ie1a_ (A:)
1b: SCOP_d3ie1b_ (B:)
1c: SCOP_d3ie1c_ (C:)
1d: SCOP_d3ie1d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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
d3ie1a_
A:
1b
d3ie1b_
B:
1c
d3ie1c_
C:
1d
d3ie1d_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
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
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (289 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
Biol.Unit 2 (75 KB)
Header - Biol.Unit 2
Biol.Unit 3 (74 KB)
Header - Biol.Unit 3
Biol.Unit 4 (75 KB)
Header - Biol.Unit 4
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3IE1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help