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4DWR
Biol. Unit 3
Info
Asym.Unit (570 KB)
Biol.Unit 1 (193 KB)
Biol.Unit 2 (189 KB)
Biol.Unit 3 (192 KB)
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(1)
Title
:
RNA LIGASE RTCB/MN2+ COMPLEX
Authors
:
S. Xia, M. Englert, D. Soll, J. Wang
Date
:
26 Feb 12 (Deposition) - 05 Sep 12 (Release) - 19 Dec 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.48
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: B (1x)
Biol. Unit 2: A (1x)
Biol. Unit 3: C (1x)
Keywords
:
Rna Ligase, Rtcb, Mn2+, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Englert, S. Xia, C. Okada, A. Nakamura, V. Tanavde, M. Yao, S. H. Eom, W. H. Konigsberg, D. Soll, J. Wang
Structural And Mechanistic Insights Into Guanylylation Of Rna-Splicing Ligase Rtcb Joining Rna Between 3'-Terminal Phosphate And 5'-Oh.
Proc. Natl. Acad. Sci. Usa V. 109 15235 2012
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
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)
3a: SUCROSE (SUCa)
3b: SUCROSE (SUCb)
3c: SUCROSE (SUCc)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MN
-1
Ligand/Ion
MANGANESE (II) ION
2
SO4
7
Ligand/Ion
SULFATE ION
3
SUC
1
Ligand/Ion
SUCROSE
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Sites
(10, 10)
Info
All Sites
01: CC3 (SOFTWARE)
02: CC4 (SOFTWARE)
03: CC5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: DC3 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
CC3
SOFTWARE
LYS C:17 , ARG C:23 , PRO C:25 , TYR C:57 , LYS C:58 , ASP C:340 , HOH C:886 , HOH C:911 , HOH C:950 , HOH C:1166 , HOH C:1200 , HOH C:1229
BINDING SITE FOR RESIDUE SUC C 601
02
CC4
SOFTWARE
CYS C:98 , HIS C:234 , HIS C:329 , HOH C:709 , HOH C:748 , HOH C:912
BINDING SITE FOR RESIDUE MN C 602
03
CC5
SOFTWARE
ASP C:95 , CYS C:98 , HIS C:203 , SO4 C:608
BINDING SITE FOR RESIDUE MN C 603
04
CC6
SOFTWARE
GLY C:69 , TYR C:70 , ILE C:74 , GLY C:93 , TYR C:94 , LYS C:351 , HOH C:746 , HOH C:1057
BINDING SITE FOR RESIDUE SO4 C 604
05
CC7
SOFTWARE
GLY C:199 , SER C:200 , HIS C:203 , ARG C:238 , GLY C:239 , HOH C:847 , HOH C:982 , HOH C:996 , HOH C:997 , HOH C:998 , HOH C:1055
BINDING SITE FOR RESIDUE SO4 C 605
06
CC8
SOFTWARE
TYR C:259 , SER C:275 , GLU C:276 , HOH C:1008
BINDING SITE FOR RESIDUE SO4 C 606
07
CC9
SOFTWARE
ARG C:366 , ARG C:369 , HOH C:1075
BINDING SITE FOR RESIDUE SO4 C 607
08
DC1
SOFTWARE
ASP C:95 , CYS C:98 , HIS C:203 , ASN C:330 , MN C:603 , HOH C:746 , HOH C:748 , HOH C:912 , HOH C:971 , HOH C:996 , HOH C:1056
BINDING SITE FOR RESIDUE SO4 C 608
09
DC2
SOFTWARE
LYS C:212 , ARG C:472 , HOH C:1063
BINDING SITE FOR RESIDUE SO4 C 609
10
DC3
SOFTWARE
SER C:411 , ARG C:412 , HOH C:811 , HOH C:1038
BINDING SITE FOR RESIDUE SO4 C 610
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: INTEIN_C_TER (C:98-98)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEIN_C_TER
PS50818
Intein C-terminal splicing motif profile.
RTCB_PYRHO
465-488
1
-
-
C:98-98
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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, 3)
Info
All SCOP Domains
1a: SCOP_d4dwra_ (A:)
1b: SCOP_d4dwrb_ (B:)
1c: SCOP_d4dwrc_ (C:)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Hypothetical protein PH1602
(7)
Superfamily
:
Hypothetical protein PH1602
(7)
Family
:
Hypothetical protein PH1602
(6)
Protein domain
:
automated matches
(1)
Pyrococcus horikoshii [TaxId: 53953]
(1)
1a
d4dwra_
A:
1b
d4dwrb_
B:
1c
d4dwrc_
C:
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CATH Domains
(0, 0)
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Pfam Domains
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Chain C
Asymmetric Unit 1
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Asym.Unit (570 KB)
Header - Asym.Unit
Biol.Unit 1 (193 KB)
Header - Biol.Unit 1
Biol.Unit 2 (189 KB)
Header - Biol.Unit 2
Biol.Unit 3 (192 KB)
Header - Biol.Unit 3
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