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1RXQ
Biol. Unit 2
Info
Asym.Unit (135 KB)
Biol.Unit 1 (127 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (66 KB)
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(1)
Title
:
YFIT FROM BACILLUS SUBTILIS IS A PROBABLE METAL-DEPENDENT HYDROLASE WITH AN UNUSUAL FOUR-HELIX BUNDLE TOPOLOGY
Authors
:
S. S. Rajan, X. Yang, W. F. Anderson, Midwest Center For Structural (Mcsg)
Date
:
18 Dec 03 (Deposition) - 20 Jul 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: A,D (1x)
Biol. Unit 3: B,C (1x)
Keywords
:
Nickel-Binding, Hydrolase, Helix-Bundle, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Metal-Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
S. S. Rajan, X. Yang, L. Shuvalova, F. Collart, W. F. Anderson
Yfit From Bacillus Subtilis Is A Probable Metal-Dependent Hydrolase With An Unusual Four-Helix Bundle Topology
Biochemistry V. 43 15472 2004
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Hetero Components
(6, 12)
Info
All Hetero Components
1a: ALANINE (ALAa)
2a: GLUTAMIC ACID (GLUa)
3a: GLYCINE (GLYa)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
5c: NICKEL (II) ION (NIc)
5d: NICKEL (II) ION (NId)
6a: SERINE (SERa)
6b: SERINE (SERb)
7a: THREONINE (THRa)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ALA
1
Mod. Amino Acid
ALANINE
2
GLU
1
Mod. Amino Acid
GLUTAMIC ACID
3
GLY
1
Mod. Amino Acid
GLYCINE
4
MSE
6
Mod. Amino Acid
SELENOMETHIONINE
5
NI
-1
Ligand/Ion
NICKEL (II) ION
6
SER
2
Mod. Amino Acid
SERINE
7
THR
1
Mod. Amino Acid
THREONINE
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
8: BC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:67 , HIS A:160 , HIS A:164 , HOH A:310 , HOH A:311 , HOH A:312
BINDING SITE FOR RESIDUE NI A 300
2
AC4
SOFTWARE
HIS D:67 , HIS D:160 , HIS D:164 , GLU D:501 , HOH D:623 , HOH D:624 , HOH D:625
BINDING SITE FOR RESIDUE NI D 300
3
AC5
SOFTWARE
TRP D:59 , HIS D:67 , GLU D:95 , HIS D:160 , HIS D:164 , NI D:300 , SER D:502 , ALA D:503 , THR D:504 , HOH D:623 , HOH D:624 , HOH D:625 , HOH D:626
BINDING SITE FOR RESIDUE GLU D 501
4
AC6
SOFTWARE
LEU D:156 , TYR D:157 , TRP D:159 , HIS D:160 , GLU D:501 , ALA D:503 , THR D:504 , HOH D:625
BINDING SITE FOR RESIDUE SER D 502
5
AC7
SOFTWARE
LEU D:156 , GLU D:501 , SER D:502 , THR D:504
BINDING SITE FOR RESIDUE ALA D 503
6
AC8
SOFTWARE
ILE C:10 , GLU D:501 , SER D:502 , ALA D:503 , SER D:505 , GLY D:506
BINDING SITE FOR RESIDUE THR D 504
7
AC9
SOFTWARE
GLY C:11 , GLU D:12 , THR D:504 , GLY D:506 , HOH D:627
BINDING SITE FOR RESIDUE SER D 505
8
BC1
SOFTWARE
ASN C:5 , TYR C:8 , THR D:504 , SER D:505
BINDING SITE FOR RESIDUE GLY D 506
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1rxqa_ (A:)
1b: SCOP_d1rxqb_ (B:)
1c: SCOP_d1rxqc_ (C:)
1d: SCOP_d1rxqd_ (D:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DinB/YfiT-like putative metalloenzymes
(8)
Superfamily
:
DinB/YfiT-like putative metalloenzymes
(8)
Family
:
YfiT-like putative metal-dependent hydrolases
(1)
Protein domain
:
YfiT
(1)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d1rxqa_
A:
1b
d1rxqb_
B:
1c
d1rxqc_
C:
1d
d1rxqd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1rxqD00 (D:10-178)
1b: CATH_1rxqA00 (A:5-178)
1c: CATH_1rxqC00 (C:5-178)
1d: CATH_1rxqB00 (B:4-178)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
dinb family like domain
(9)
Bacillus subtilis. Organism_taxid: 1423.
(1)
1a
1rxqD00
D:10-178
1b
1rxqA00
A:5-178
1c
1rxqC00
C:5-178
1d
1rxqB00
B:4-178
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DinB_2_1rxqD01 (D:30-168)
1b: PFAM_DinB_2_1rxqD02 (D:30-168)
1c: PFAM_DinB_2_1rxqD03 (D:30-168)
1d: PFAM_DinB_2_1rxqD04 (D:30-168)
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Clan
:
DinB
(11)
Family
:
DinB_2
(5)
Bacillus subtilis
(1)
1a
DinB_2-1rxqD01
D:30-168
1b
DinB_2-1rxqD02
D:30-168
1c
DinB_2-1rxqD03
D:30-168
1d
DinB_2-1rxqD04
D:30-168
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (135 KB)
Header - Asym.Unit
Biol.Unit 1 (127 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (66 KB)
Header - Biol.Unit 3
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