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2WBM
Biol. Unit 2
Info
Asym.Unit (92 KB)
Biol.Unit 1 (45 KB)
Biol.Unit 2 (44 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MTHSBDS, THE HOMOLOGUE OF THE SHWACHMAN-BODIAN-DIAMOND SYNDROME PROTEIN IN THE EURIARCHAEON METHANOTHERMOBACTER THERMAUTOTROPHICUS
Authors
:
C. L. Ng, M. N. Isupov, A. A. Lebedev, M. Ortiz-Lombardia, A. A. Antson
Date
:
02 Mar 09 (Deposition) - 02 Jun 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Shwachman-Bodian-Diamond Syndrome Protein, Ribosome Binding, Conformational Flexibility, Rna-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. L. Ng, D. G. Waterman, E. V. Koonin, A. D. Walters, J. P. Chong, M. N. Isupov, A. A. Lebedev, D. H. Bunka, P. G. Stockley, M. Ortiz-Lombardia, A. A. Antson
Conformational Flexibility And Molecular Interactions Of An Archaeal Homologue Of The Shwachman-Bodian-Diamond Syndrome Protein.
Bmc Struct. Biol. V. 9 32 2009
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Hetero Components
(2, 5)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
SO4
3
Ligand/Ion
SULFATE ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: AC9 (SOFTWARE)
6: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA B:168 , LEU B:230 , LYS B:232 , HOH B:2172 , HOH B:2173 , HOH B:2174 , HOH B:2175
BINDING SITE FOR RESIDUE GOL B1233
2
AC3
SOFTWARE
LYS B:164 , GLY B:187 , LYS B:188 , GLU B:205 , PRO B:207
BINDING SITE FOR RESIDUE GOL B1234
3
AC7
SOFTWARE
ARG A:65 , HOH A:2082 , GLN B:195 , ARG B:229 , HOH B:2181 , HOH B:2182 , HOH B:2183
BINDING SITE FOR RESIDUE SO4 B1238
4
AC8
SOFTWARE
LYS B:103 , ASN B:106 , ARG B:110 , HOH B:2176 , HOH B:2177
BINDING SITE FOR RESIDUE SO4 B1235
5
AC9
SOFTWARE
ARG B:11 , GLN B:87 , HOH B:2178 , HOH B:2179
BINDING SITE FOR RESIDUE SO4 B1236
6
BC1
SOFTWARE
ILE B:160 , LYS B:161
BINDING SITE FOR RESIDUE CL B1237
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: UPF0023 (B:38-56)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UPF0023
PS01267
Uncharacterized protein family UPF0023 signature.
SDO1_METTH
37-56
1
-
B:38-56
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Exons
(0, 0)
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d2wbma2 (A:88-162)
1b: SCOP_d2wbmb2 (B:88-162)
2a: SCOP_d2wbma3 (A:163-232)
2b: SCOP_d2wbmb3 (B:163-232)
3a: SCOP_d2wbma1 (A:-1-87)
3b: SCOP_d2wbmb1 (B:1-87)
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Protein Domains
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
RuvA C-terminal domain-like
(106)
Superfamily
:
Hypothetical protein AF0491, middle domain
(3)
Family
:
automated matches
(1)
Protein domain
:
automated matches
(1)
Methanothermobacter thermautotrophicus [TaxId: 187420]
(1)
1a
d2wbma2
A:88-162
1b
d2wbmb2
B:88-162
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
EF-G C-terminal domain-like
(33)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Methanothermobacter thermautotrophicus [TaxId: 187420]
(1)
2a
d2wbma3
A:163-232
2b
d2wbmb3
B:163-232
Fold
:
FYSH domain
(4)
Superfamily
:
FYSH domain
(4)
Family
:
automated matches
(1)
Protein domain
:
automated matches
(1)
Methanothermobacter thermautotrophicus [TaxId: 187420]
(1)
3a
d2wbma1
A:-1-87
3b
d2wbmb1
B:1-87
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2wbmA01 (A:7-87)
1b: CATH_2wbmB01 (B:7-87)
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Topologies
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Hypothetical 12.0 Kda Protein In Nam8-gar1 Intergenic Region; Chain: A;
(4)
Homologous Superfamily
:
[code=3.30.1250.10, no name defined]
(4)
Methanothermobacter thermautotrophicus. Organism_taxid: 187420. Strain: delta h.
(1)
1a
2wbmA01
A:7-87
1b
2wbmB01
B:7-87
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_SBDS_C_2wbmB01 (B:99-221)
1b: PFAM_SBDS_C_2wbmB02 (B:99-221)
2a: PFAM_SBDS_2wbmB03 (B:5-96)
2b: PFAM_SBDS_2wbmB04 (B:5-96)
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Clans
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Clan
:
EF-G_C
(20)
Family
:
SBDS_C
(5)
Methanobacterium thermoautotrophicum (strain Delta H)
(1)
1a
SBDS_C-2wbmB01
B:99-221
1b
SBDS_C-2wbmB02
B:99-221
Clan
:
no clan defined [family: SBDS]
(6)
Family
:
SBDS
(6)
Methanobacterium thermoautotrophicum (strain Delta H)
(1)
2a
SBDS-2wbmB03
B:5-96
2b
SBDS-2wbmB04
B:5-96
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Chain B
Asymmetric Unit 1
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Asym.Unit (92 KB)
Header - Asym.Unit
Biol.Unit 1 (45 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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