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1OKJ
Biol. Unit 1
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Asym.Unit (148 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (73 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ESSENTIAL E. COLI YEAZ PROTEIN BY MAD METHOD USING THE GADOLINIUM COMPLEX "DOTMA"
Authors
:
C. Abergel, S. Jeudy, J. M. Claverie
Date
:
26 Jul 03 (Deposition) - 16 Sep 04 (Release) - 23 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.28
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Potential Zinc Protease, Hypothetical Protease Yeaz, Metalloprotease, Hydrolase, Bacterial Targets At Igs-Cnrs, France, Bigs, Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Stelter, R. Molina, S. Jeudy, R. Kahn, C. Abergel, J. A. Hermoso
A Complement To The Modern Crystallographer'S Toolbox: Caged Gadolinium Complexes With Versatile Binding Modes.
Acta Crystallogr. , Sect. D V. 70 1506 2014
(for further references see the
PDB file header
)
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Hetero Components
(1, 8)
Info
All Hetero Components
1a: GADOLINIUM ION (GD3a)
1b: GADOLINIUM ION (GD3b)
1c: GADOLINIUM ION (GD3c)
1d: GADOLINIUM ION (GD3d)
1e: GADOLINIUM ION (GD3e)
1f: GADOLINIUM ION (GD3f)
1g: GADOLINIUM ION (GD3g)
1h: GADOLINIUM ION (GD3h)
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No.
Name
Count
Type
Full Name
1
GD3
8
Ligand/Ion
GADOLINIUM ION
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Sites
(3, 3)
Info
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH B:2029
BINDING SITE FOR RESIDUE GD3 A1214
2
AC2
SOFTWARE
ARG B:31
BINDING SITE FOR RESIDUE GD3 A1216
3
AC3
SOFTWARE
ARG A:31
BINDING SITE FOR RESIDUE GD3 A1218
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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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PROSITE Patterns/Profiles
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Exons
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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, 8)
Info
All SCOP Domains
1a: SCOP_d1okja1 (A:1-106)
1b: SCOP_d1okja2 (A:107-216)
1c: SCOP_d1okjb1 (B:1-106)
1d: SCOP_d1okjb2 (B:107-216)
1e: SCOP_d1okjc1 (C:1-106)
1f: SCOP_d1okjc2 (C:107-216)
1g: SCOP_d1okjd1 (D:1-106)
1h: SCOP_d1okjd2 (D:107-216)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Actin-like ATPase domain
(426)
Family
:
YeaZ-like
(2)
Protein domain
:
Hypothetical protein YeaZ
(1)
Escherichia coli [TaxId: 562]
(1)
1a
d1okja1
A:1-106
1b
d1okja2
A:107-216
1c
d1okjb1
B:1-106
1d
d1okjb2
B:107-216
1e
d1okjc1
C:1-106
1f
d1okjc2
C:107-216
1g
d1okjd1
D:1-106
1h
d1okjd2
D:107-216
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1okjB01 (B:-4-92,B:188-218)
1b: CATH_1okjD01 (D:-2-92,D:188-218)
1c: CATH_1okjA01 (A:-1-92,A:188-218)
1d: CATH_1okjC01 (C:-1-92,C:188-217)
1e: CATH_1okjA02 (A:93-187)
1f: CATH_1okjB02 (B:93-187)
1g: CATH_1okjC02 (C:93-187)
1h: CATH_1okjD02 (D:93-187)
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Organisms
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(
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Nucleotidyltransferase; domain 5
(788)
Homologous Superfamily
:
[code=3.30.420.40, no name defined]
(217)
Escherichia coli. Organism_taxid: 83333. Strain: k12.
(1)
1a
1okjB01
B:-4-92,B:188-218
1b
1okjD01
D:-2-92,D:188-218
1c
1okjA01
A:-1-92,A:188-218
1d
1okjC01
C:-1-92,C:188-217
1e
1okjA02
A:93-187
1f
1okjB02
B:93-187
1g
1okjC02
C:93-187
1h
1okjD02
D:93-187
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (148 KB)
Header - Asym.Unit
Biol.Unit 1 (74 KB)
Header - Biol.Unit 1
Biol.Unit 2 (73 KB)
Header - Biol.Unit 2
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