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3SHD
Biol. Unit 11
Info
Asym.Unit (314 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 10 (31 KB)
Biol.Unit 11 (31 KB)
Biol.Unit 12 (31 KB)
Biol.Unit 13 (57 KB)
Biol.Unit 14 (56 KB)
Biol.Unit 15 (57 KB)
Biol.Unit 16 (57 KB)
Biol.Unit 17 (56 KB)
Biol.Unit 18 (56 KB)
Biol.Unit 2 (31 KB)
Biol.Unit 3 (31 KB)
Biol.Unit 4 (31 KB)
Biol.Unit 5 (32 KB)
Biol.Unit 6 (31 KB)
Biol.Unit 7 (31 KB)
Biol.Unit 8 (31 KB)
Biol.Unit 9 (31 KB)
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Title
:
CRYSTAL STRUCTURE OF NUDIX HYDROLASE ORF153, YMFB, FROM ESCHERICHIA COLI K-1
Authors
:
M. K. Hong, J. K. Kim, L. W. Kang
Date
:
16 Jun 11 (Deposition) - 27 Jun 12 (Release) - 27 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Biol. Unit 10: J (1x)
Biol. Unit 11: K (1x)
Biol. Unit 12: L (1x)
Biol. Unit 13: A,I (1x)
Biol. Unit 14: B,L (1x)
Biol. Unit 15: C,G (1x)
Biol. Unit 16: D,E (1x)
Biol. Unit 17: F,K (1x)
Biol. Unit 18: H,J (1x)
Keywords
:
Nudix Fold, Nudix Motif, Hydrolase, (D)Ndp/(D)Ntp Binding, Dephosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. K. Hong
Structure And Atypical Hydrolysis Mechanism Of The Nudix Hydrolase Orf153 (Ymfb) From Escherichia Coli
To Be Published
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
1i: MANGANESE (II) ION (MNi)
1j: MANGANESE (II) ION (MNj)
1k: MANGANESE (II) ION (MNk)
1l: MANGANESE (II) ION (MNl)
1m: MANGANESE (II) ION (MNm)
1n: MANGANESE (II) ION (MNn)
1o: MANGANESE (II) ION (MNo)
1p: MANGANESE (II) ION (MNp)
1q: MANGANESE (II) ION (MNq)
1r: MANGANESE (II) ION (MNr)
1s: MANGANESE (II) ION (MNs)
1t: MANGANESE (II) ION (MNt)
1u: MANGANESE (II) ION (MNu)
1v: MANGANESE (II) ION (MNv)
1w: MANGANESE (II) ION (MNw)
1x: MANGANESE (II) ION (MNx)
2a: SULFATE ION (SO4a)
2aa: SULFATE ION (SO4aa)
2ab: SULFATE ION (SO4ab)
2ac: SULFATE ION (SO4ac)
2ad: SULFATE ION (SO4ad)
2ae: SULFATE ION (SO4ae)
2af: SULFATE ION (SO4af)
2ag: SULFATE ION (SO4ag)
2ah: SULFATE ION (SO4ah)
2ai: SULFATE ION (SO4ai)
2aj: SULFATE ION (SO4aj)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
2w: SULFATE ION (SO4w)
2x: SULFATE ION (SO4x)
2y: SULFATE ION (SO4y)
2z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
-1
Ligand/Ion
MANGANESE (II) ION
2
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: FC6 (SOFTWARE)
2: FC7 (SOFTWARE)
3: FC8 (SOFTWARE)
4: FC9 (SOFTWARE)
5: GC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
FC6
SOFTWARE
GLU K:51 , GLU K:55 , MN K:155 , SO4 K:156 , SO4 K:157 , HOH K:178 , HOH K:204
BINDING SITE FOR RESIDUE MN K 154
2
FC7
SOFTWARE
GLU K:51 , MN K:154 , SO4 K:156
BINDING SITE FOR RESIDUE MN K 155
3
FC8
SOFTWARE
GLY K:36 , HIS K:37 , GLU K:51 , MN K:154 , MN K:155 , SO4 K:157 , HOH K:172
BINDING SITE FOR RESIDUE SO4 K 156
4
FC9
SOFTWARE
GLU K:23 , ASN K:32 , ALA K:35 , GLY K:36 , GLU K:51 , GLU K:55 , MN K:154 , SO4 K:156 , SO4 K:158 , HOH K:178
BINDING SITE FOR RESIDUE SO4 K 157
5
GC1
SOFTWARE
THR K:7 , ASN K:32 , ALA K:35 , GLY K:36 , ARG K:81 , SO4 K:157
BINDING SITE FOR RESIDUE SO4 K 158
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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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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NUDIX (K:3-131)
2: NUDIX_BOX (K:36-57)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NUDIX
PS51462
Nudix hydrolase domain profile.
NUDJ_ECOK1
3-131
1
-
-
-
-
-
-
-
-
-
-
K:3-131
-
2
NUDIX_BOX
PS00893
Nudix box signature.
NUDJ_ECOK1
36-57
1
-
-
-
-
-
-
-
-
-
-
K:36-57
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3shda_ (A:)
1b: SCOP_d3shdc_ (C:)
1c: SCOP_d3shdd_ (D:)
1d: SCOP_d3shde_ (E:)
1e: SCOP_d3shdf_ (F:)
1f: SCOP_d3shdg_ (G:)
1g: SCOP_d3shdh_ (H:)
1h: SCOP_d3shdi_ (I:)
1i: SCOP_d3shdj_ (J:)
1j: SCOP_d3shdk_ (K:)
1k: SCOP_d3shdl_ (L:)
1l: SCOP_d3shdb_ (B:)
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Protein Domains
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Nudix
(141)
Superfamily
:
Nudix
(141)
Family
:
automated matches
(20)
Protein domain
:
automated matches
(20)
Escherichia coli [TaxId: 405955]
(2)
1a
d3shda_
A:
1b
d3shdc_
C:
1c
d3shdd_
D:
1d
d3shde_
E:
1e
d3shdf_
F:
1f
d3shdg_
G:
1g
d3shdh_
H:
1h
d3shdi_
I:
1i
d3shdj_
J:
1j
d3shdk_
K:
1k
d3shdl_
L:
1l
d3shdb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
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Pfam Domains
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Sorry, no Info available
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Chain K
Asymmetric Unit 1
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