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1O87
Biol. Unit 1
Info
Asym.Unit (107 KB)
Biol.Unit 1 (52 KB)
Biol.Unit 2 (52 KB)
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(1)
Title
:
A NEW MGGDP COMPLEX OF THE FFH NG DOMAIN
Authors
:
D. M. Freymann
Date
:
25 Nov 02 (Deposition) - 02 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein Transport, Ffh, Signal Recognition Particle, Srp, Gtpase, Gtp-Binding, Rna-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. J. Focia, H. Alam, T. Lu, U. D. Ramirez, D. M. Freymann
Novel Protein And Mg2+ Configurations In The Mg2+Gdp Complex Of The Srp Gtpase Ffh
Proteins: Struct. , Funct. , V. 54 222 2004 Genet.
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: FORMIC ACID (FMTa)
2b: FORMIC ACID (FMTb)
2c: FORMIC ACID (FMTc)
2d: FORMIC ACID (FMTd)
2e: FORMIC ACID (FMTe)
3a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
3b: GUANOSINE-5'-DIPHOSPHATE (GDPb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
FMT
2
Ligand/Ion
FORMIC ACID
3
GDP
1
Ligand/Ion
GUANOSINE-5'-DIPHOSPHATE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC8 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:32 , ARG A:36
BINDING SITE FOR RESIDUE CL A1296
2
AC2
SOFTWARE
THR A:112 , GDP A:1299 , HOH A:2055 , HOH A:2074 , HOH A:2127 , HOH A:2128
BINDING SITE FOR RESIDUE MG A1300
3
AC3
SOFTWARE
ASP A:212 , HOH A:2090 , HOH A:2091 , HOH A:2092
BINDING SITE FOR RESIDUE MG A1301
4
AC6
SOFTWARE
LEU A:106 , GLY A:108 , SER A:109 , GLY A:110 , LYS A:111 , THR A:112 , THR A:113 , LYS A:117 , GLN A:144 , LYS A:246 , ASP A:248 , GLY A:271 , VAL A:272 , SER A:273 , GLU A:274 , MG A:1300 , HOH A:2056 , HOH A:2127 , HOH A:2128 , HOH A:2129
BINDING SITE FOR RESIDUE GDP A1299
5
AC8
SOFTWARE
PRO A:281 , ARG A:286 , SER B:67 , THR B:69 , VAL B:73
BINDING SITE FOR RESIDUE FMT A1297
6
AC9
SOFTWARE
ARG A:191 , GLN A:193 , ASP A:195 , LEU A:198 , MET A:199
BINDING SITE FOR RESIDUE FMT A1298
7
BC2
SOFTWARE
SER A:67 , THR A:69 , VAL A:73 , PRO B:281 , ARG B:286 , HOH B:2134 , HOH B:2142
BINDING SITE FOR RESIDUE FMT B1297
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SRP54 (A:266-279)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SRP54
PS00300
SRP54-type proteins GTP-binding domain signature.
SRP54_THEAQ
266-279
1
A:266-279
-
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1o87a1 (A:1-88)
1b: SCOP_d1o87b1 (B:1-88)
2a: SCOP_d1o87a2 (A:89-295)
2b: SCOP_d1o87b2 (B:89-295)
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(
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Domain of the SRP/SRP receptor G-proteins
(34)
Family
:
Domain of the SRP/SRP receptor G-proteins
(29)
Protein domain
:
Signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
1a
d1o87a1
A:1-88
1b
d1o87b1
B:1-88
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
:
Nitrogenase iron protein-like
(152)
Protein domain
:
GTPase domain of the signal sequence recognition protein Ffh
(21)
Thermus aquaticus [TaxId: 271]
(17)
2a
d1o87a2
A:89-295
2b
d1o87b2
B:89-295
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1o87A02 (A:91-281)
1b: CATH_1o87B02 (B:91-281)
2a: CATH_1o87A01 (A:2-90)
2b: CATH_1o87B01 (B:2-90)
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Thermus aquaticus. Organism_taxid: 271.
(14)
1a
1o87A02
A:91-281
1b
1o87B02
B:91-281
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.140, no name defined]
(15)
Thermus aquaticus. Organism_taxid: 271.
(6)
2a
1o87A01
A:2-90
2b
1o87B01
B:2-90
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_SRP54_1o87B01 (B:98-293)
1b: PFAM_SRP54_1o87B02 (B:98-293)
2a: PFAM_SRP54_N_1o87B03 (B:5-82)
2b: PFAM_SRP54_N_1o87B04 (B:5-82)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
SRP54
(20)
Thermus aquaticus
(12)
1a
SRP54-1o87B01
B:98-293
1b
SRP54-1o87B02
B:98-293
Clan
:
no clan defined [family: SRP54_N]
(20)
Family
:
SRP54_N
(20)
Thermus aquaticus
(12)
2a
SRP54_N-1o87B03
B:5-82
2b
SRP54_N-1o87B04
B:5-82
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Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (107 KB)
Header - Asym.Unit
Biol.Unit 1 (52 KB)
Header - Biol.Unit 1
Biol.Unit 2 (52 KB)
Header - Biol.Unit 2
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