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2RD9
Asym. Unit
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Asym.Unit (151 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (73 KB)
Biol.Unit 3 (142 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A PUTATIVE YFIT-LIKE METAL-DEPENDENT HYDROLASE (BH0186) FROM BACILLUS HALODURANS C-125 AT 2.30 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
21 Sep 07 (Deposition) - 09 Oct 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Yfit-Like Putative Metal-Dependent Hydrolase (Np_241052. 1) From Bacillus Halodurans At 2. 30 A Resolution
To Be Published
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Hetero Components
(4, 28)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
2a: IMIDAZOLE (IMDa)
2b: IMIDAZOLE (IMDb)
2c: IMIDAZOLE (IMDc)
2d: IMIDAZOLE (IMDd)
2e: IMIDAZOLE (IMDe)
3a: SELENOMETHIONINE (MSEa)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
4a: NICKEL (II) ION (NIa)
4b: NICKEL (II) ION (NIb)
4c: NICKEL (II) ION (NIc)
4d: NICKEL (II) ION (NId)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
IMD
5
Ligand/Ion
IMIDAZOLE
3
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
4
NI
4
Ligand/Ion
NICKEL (II) ION
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Sites
(15, 15)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:48 , HIS A:142 , HIS A:146 , IMD A:301 , HOH A:421 , HIS D:-9
BINDING SITE FOR RESIDUE NI A 300
02
AC2
SOFTWARE
HIS B:-9 , HIS C:48 , HIS C:142 , HIS C:146 , IMD C:302 , HOH C:384
BINDING SITE FOR RESIDUE NI C 300
03
AC3
SOFTWARE
IMD A:303 , HOH A:393 , HIS B:48 , HIS B:142 , HIS B:146 , HIS C:-9
BINDING SITE FOR RESIDUE NI B 300
04
AC4
SOFTWARE
HIS A:-9 , IMD C:301 , HOH C:382 , HIS D:48 , HIS D:142 , HIS D:146
BINDING SITE FOR RESIDUE NI D 300
05
AC5
SOFTWARE
HIS A:142 , HIS A:146 , NI A:300 , HOH A:421 , TYR B:168 , LEU B:169 , ILE B:171 , HIS D:-9
BINDING SITE FOR RESIDUE IMD A 301
06
AC6
SOFTWARE
HIS A:-9 , TYR C:168 , LEU C:169 , ILE C:171 , HOH C:382 , HIS D:142 , HIS D:146 , NI D:300
BINDING SITE FOR RESIDUE IMD C 301
07
AC7
SOFTWARE
HIS B:-9 , HIS C:142 , HIS C:146 , NI C:300 , TYR D:168 , LEU D:169 , ILE D:171
BINDING SITE FOR RESIDUE IMD C 302
08
AC8
SOFTWARE
MSE A:5 , GLN A:113 , SER A:114 , ARG B:78
BINDING SITE FOR RESIDUE IMD A 302
09
AC9
SOFTWARE
TYR A:168 , LEU A:169 , ILE A:171 , HOH A:393 , HOH A:394 , HIS B:142 , HIS B:146 , NI B:300 , HIS C:-9
BINDING SITE FOR RESIDUE IMD A 303
10
BC1
SOFTWARE
TRP A:40 , GLU A:44 , HOH A:355
BINDING SITE FOR RESIDUE GOL A 304
11
BC2
SOFTWARE
GLN A:-1 , TYR A:-3 , LEU A:-4 , GLY B:36 , TYR B:37 , LYS B:156 , GLU C:167
BINDING SITE FOR RESIDUE GOL A 305
12
BC3
SOFTWARE
PHE A:79 , SER A:80 , HOH A:362 , MSE D:5 , ARG D:109 , HOH D:348 , HOH D:428 , HOH D:436
BINDING SITE FOR RESIDUE GOL D 301
13
BC4
SOFTWARE
ALA B:116 , GLU B:119 , ARG B:120 , PHE C:63 , GLN C:66 , GLU C:67 , HOH C:380
BINDING SITE FOR RESIDUE GOL B 301
14
BC5
SOFTWARE
HIS A:-12 , HOH A:405 , TRP D:40 , GLU D:44 , GLU D:51 , HOH D:396
BINDING SITE FOR RESIDUE GOL D 302
15
BC6
SOFTWARE
TYR C:43 , ASN C:86 , ALA C:87 , VAL C:88 , PRO C:89 , ILE C:90 , HOH C:360 , HOH C:417
BINDING SITE FOR RESIDUE GOL C 303
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Sorry, no Info available
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2rd9B01 (B:-9-171)
1b: CATH_2rd9A01 (A:-9-171)
1c: CATH_2rd9C01 (C:-9-171)
1d: CATH_2rd9D01 (D:-9-171)
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Organisms
(
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(
)
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 halodurans c-125. Organism_taxid: 272558. Strain: c-125, dsm18197, ferm 7344, jcm 9153.
(1)
1a
2rd9B01
B:-9-171
1b
2rd9A01
A:-9-171
1c
2rd9C01
C:-9-171
1d
2rd9D01
D:-9-171
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DinB_2_2rd9D01 (D:11-150)
1b: PFAM_DinB_2_2rd9D02 (D:11-150)
1c: PFAM_DinB_2_2rd9D03 (D:11-150)
1d: PFAM_DinB_2_2rd9D04 (D:11-150)
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Clans
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Clan
:
DinB
(11)
Family
:
DinB_2
(5)
Bacillus halodurans
(1)
1a
DinB_2-2rd9D01
D:11-150
1b
DinB_2-2rd9D02
D:11-150
1c
DinB_2-2rd9D03
D:11-150
1d
DinB_2-2rd9D04
D:11-150
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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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Asym.Unit (151 KB)
Header - Asym.Unit
Biol.Unit 1 (72 KB)
Header - Biol.Unit 1
Biol.Unit 2 (73 KB)
Header - Biol.Unit 2
Biol.Unit 3 (142 KB)
Header - Biol.Unit 3
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