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1OYP
Biol. Unit 1
Info
Asym.Unit (214 KB)
Biol.Unit 1 (208 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PHOSPHOROLYTIC EXORIBONUCLEASE RNASE PH FROM BACILLUS SUBTILIS
Authors
:
L. S. Harlow, A. Kadziola, K. F. Jensen, S. Larsen
Date
:
07 Apr 03 (Deposition) - 09 Mar 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.76
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Transferase, Trna Processing
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. S. Harlow, A. Kadziola, K. F. Jensen, S. Larsen
Crystal Structure Of The Phosphorolytic Exoribonuclease Rnase Ph From Bacillus Subtilis And Implications For Its Quaternary Structure And Trna Binding.
Protein Sci. V. 13 668 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
1c: SULFATE ION (SO4c)
1d: SULFATE ION (SO4d)
1e: SULFATE ION (SO4e)
1f: SULFATE ION (SO4f)
1g: SULFATE ION (SO4g)
1h: SULFATE ION (SO4h)
1i: SULFATE ION (SO4i)
1j: SULFATE ION (SO4j)
1k: SULFATE ION (SO4k)
1l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
12
Ligand/Ion
SULFATE ION
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:86 , GLY A:124 , THR A:125 , ARG A:126
BINDING SITE FOR RESIDUE SO4 A 301
02
AC2
SOFTWARE
TRP A:58 , THR A:60 , ARG A:99
BINDING SITE FOR RESIDUE SO4 A 302
03
AC3
SOFTWARE
ARG B:86 , GLY B:124 , THR B:125 , ARG B:126
BINDING SITE FOR RESIDUE SO4 B 303
04
AC4
SOFTWARE
TRP B:58 , THR B:60 , ARG B:99
BINDING SITE FOR RESIDUE SO4 B 304
05
AC5
SOFTWARE
ARG C:86 , GLY C:124 , THR C:125 , ARG C:126
BINDING SITE FOR RESIDUE SO4 C 305
06
AC6
SOFTWARE
TRP C:58 , THR C:60 , ARG C:99
BINDING SITE FOR RESIDUE SO4 C 306
07
AC7
SOFTWARE
ARG D:86 , GLY D:124 , THR D:125 , ARG D:126
BINDING SITE FOR RESIDUE SO4 D 307
08
AC8
SOFTWARE
TRP D:58 , THR D:60 , ARG D:99
BINDING SITE FOR RESIDUE SO4 D 308
09
AC9
SOFTWARE
ARG E:86 , GLY E:124 , THR E:125 , ARG E:126
BINDING SITE FOR RESIDUE SO4 E 309
10
BC1
SOFTWARE
TRP E:58 , THR E:60 , ARG E:99
BINDING SITE FOR RESIDUE SO4 E 310
11
BC2
SOFTWARE
ARG F:86 , GLY F:124 , THR F:125 , ARG F:126
BINDING SITE FOR RESIDUE SO4 F 311
12
BC3
SOFTWARE
TRP F:58 , THR F:60 , ARG F:99
BINDING SITE FOR RESIDUE SO4 F 312
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: RIBONUCLEASE_PH (A:116-128,B:116-128,C:116-128,D:11...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBONUCLEASE_PH
PS01277
Ribonuclease PH signature.
RNPH_BACSU
116-128
6
A:116-128
B:116-128
C:116-128
D:116-128
E:116-128
F:116-128
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 12)
Info
All SCOP Domains
1a: SCOP_d1oypa2 (A:152-243)
1b: SCOP_d1oypb2 (B:152-243)
1c: SCOP_d1oypc2 (C:152-243)
1d: SCOP_d1oypd2 (D:152-243)
1e: SCOP_d1oype2 (E:152-243)
1f: SCOP_d1oypf2 (F:152-243)
2a: SCOP_d1oypa1 (A:1-151)
2b: SCOP_d1oypb1 (B:1-151)
2c: SCOP_d1oypc1 (C:1-151)
2d: SCOP_d1oypd1 (D:1-151)
2e: SCOP_d1oype1 (E:1-151)
2f: SCOP_d1oypf1 (F:1-151)
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)
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)
Folds
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)
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)
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)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ribonuclease PH domain 2-like
(52)
Superfamily
:
Ribonuclease PH domain 2-like
(52)
Family
:
Ribonuclease PH domain 2-like
(41)
Protein domain
:
Ribonuclease PH, domain 2
(10)
Bacillus subtilis [TaxId: 1423]
(3)
1a
d1oypa2
A:152-243
1b
d1oypb2
B:152-243
1c
d1oypc2
C:152-243
1d
d1oypd2
D:152-243
1e
d1oype2
E:152-243
1f
d1oypf2
F:152-243
Fold
:
Ribosomal protein S5 domain 2-like
(306)
Superfamily
:
Ribosomal protein S5 domain 2-like
(306)
Family
:
Ribonuclease PH domain 1-like
(45)
Protein domain
:
Ribonuclease PH, domain 1
(10)
Bacillus subtilis [TaxId: 1423]
(3)
2a
d1oypa1
A:1-151
2b
d1oypb1
B:1-151
2c
d1oypc1
C:1-151
2d
d1oypd1
D:1-151
2e
d1oype1
E:1-151
2f
d1oypf1
F:1-151
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_RNase_PH_1oypF01 (F:10-141)
1b: PFAM_RNase_PH_1oypF02 (F:10-141)
1c: PFAM_RNase_PH_1oypF03 (F:10-141)
1d: PFAM_RNase_PH_1oypF04 (F:10-141)
1e: PFAM_RNase_PH_1oypF05 (F:10-141)
1f: PFAM_RNase_PH_1oypF06 (F:10-141)
2a: PFAM_RNase_PH_C_1oypF07 (F:157-225)
2b: PFAM_RNase_PH_C_1oypF08 (F:157-225)
2c: PFAM_RNase_PH_C_1oypF09 (F:157-225)
2d: PFAM_RNase_PH_C_1oypF10 (F:157-225)
2e: PFAM_RNase_PH_C_1oypF11 (F:157-225)
2f: PFAM_RNase_PH_C_1oypF12 (F:157-225)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
S5
(103)
Family
:
RNase_PH
(9)
Bacillus subtilis
(2)
1a
RNase_PH-1oypF01
F:10-141
1b
RNase_PH-1oypF02
F:10-141
1c
RNase_PH-1oypF03
F:10-141
1d
RNase_PH-1oypF04
F:10-141
1e
RNase_PH-1oypF05
F:10-141
1f
RNase_PH-1oypF06
F:10-141
Clan
:
no clan defined [family: RNase_PH_C]
(9)
Family
:
RNase_PH_C
(9)
Bacillus subtilis
(2)
2a
RNase_PH_C-1oypF07
F:157-225
2b
RNase_PH_C-1oypF08
F:157-225
2c
RNase_PH_C-1oypF09
F:157-225
2d
RNase_PH_C-1oypF10
F:157-225
2e
RNase_PH_C-1oypF11
F:157-225
2f
RNase_PH_C-1oypF12
F:157-225
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