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2ZZD
Asym. Unit
Info
Asym.Unit (392 KB)
Biol.Unit 1 (384 KB)
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(1)
Title
:
RECOMBINANT THIOCYANATE HYDROLASE, AIR-OXIDIZED FORM OF HOLO-ENZYME
Authors
:
T. Arakawa, Y. Kawano, Y. Katayama, M. Yohda, M. Odaka
Date
:
09 Feb 09 (Deposition) - 13 Oct 09 (Release) - 20 Oct 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Scnase, Hydrolase, Cobalt, Metalloprotein, Sulfenic Acid, Sulfinic Acid, Nitrile Hydratase, Thiocyanate, Carbonyl Sulfide, Claw Setting, Protein, Enzyme, Complex, Model Complex, Non-Corrin, Post-Translational Modification, Sulfenate, Sulfinate, Cysteine, Oxidation, Autocatalytic Activation, Air Inactivation, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Arakawa, Y. Kawano, Y. Katayama, H. Nakayama, N. Dohmae, M. Yohda, M. Odaka
Structural Basis For Catalytic Activation Of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification
J. Am. Chem. Soc. V. 131 14838 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 20)
Info
All Hetero Components
1a: COBALT (III) ION (3COa)
1b: COBALT (III) ION (3COb)
1c: COBALT (III) ION (3COc)
1d: COBALT (III) ION (3COd)
2a: BETA-D-GLUCOSE (BGCa)
3a: 3-SULFINOALANINE (CSDa)
3b: 3-SULFINOALANINE (CSDb)
3c: 3-SULFINOALANINE (CSDc)
3d: 3-SULFINOALANINE (CSDd)
3e: 3-SULFINOALANINE (CSDe)
3f: 3-SULFINOALANINE (CSDf)
3g: 3-SULFINOALANINE (CSDg)
3h: 3-SULFINOALANINE (CSDh)
4a: FRUCTOSE (FRUa)
4b: FRUCTOSE (FRUb)
4c: FRUCTOSE (FRUc)
5a: L(+)-TARTARIC ACID (TLAa)
5b: L(+)-TARTARIC ACID (TLAb)
5c: L(+)-TARTARIC ACID (TLAc)
5d: L(+)-TARTARIC ACID (TLAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3CO
4
Ligand/Ion
COBALT (III) ION
2
BGC
1
Ligand/Ion
BETA-D-GLUCOSE
3
CSD
8
Mod. Amino Acid
3-SULFINOALANINE
4
FRU
3
Ligand/Ion
FRUCTOSE
5
TLA
4
Ligand/Ion
L(+)-TARTARIC ACID
[
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Sites
(12, 12)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:10 , LEU B:13 , HOH B:825 , HOH B:1553 , HOH B:2421 , HOH D:215 , ARG F:157
BINDING SITE FOR RESIDUE FRU B 6002
02
AC2
SOFTWARE
CYS C:128 , CSD C:131 , SER C:132 , CSD C:133 , HOH C:244
BINDING SITE FOR RESIDUE 3CO C 301
03
AC3
SOFTWARE
VAL A:68 , ARG C:177 , HOH C:625 , HOH C:628 , HOH C:762 , HOH C:904 , HOH C:1029 , HOH C:1122 , HOH C:1318
BINDING SITE FOR RESIDUE TLA C 4001
04
AC4
SOFTWARE
CYS F:128 , CSD F:131 , SER F:132 , CSD F:133 , HOH F:244
BINDING SITE FOR RESIDUE 3CO F 301
05
AC5
SOFTWARE
VAL D:68 , ARG F:177 , HOH F:463 , HOH F:761 , HOH F:779 , HOH F:802 , HOH F:920 , HOH F:1042 , HOH F:1179
BINDING SITE FOR RESIDUE TLA F 4002
06
AC6
SOFTWARE
HOH B:2586 , GLU C:36 , ILE C:39 , ALA C:46 , HOH C:970 , HOH C:1669 , THR F:98 , HOH F:816 , HOH F:1217 , HOH F:1604 , HOH F:1740 , HOH F:3178
BINDING SITE FOR RESIDUE BGC F 5001
07
AC7
SOFTWARE
CYS I:128 , CSD I:131 , SER I:132 , CSD I:133 , HOH I:244
BINDING SITE FOR RESIDUE 3CO I 301
08
AC8
SOFTWARE
VAL G:68 , ARG I:177 , HOH I:480 , HOH I:774 , HOH I:855 , HOH I:863 , HOH I:961 , HOH I:985 , HOH I:1044
BINDING SITE FOR RESIDUE TLA I 4003
09
AC9
SOFTWARE
CYS L:128 , CSD L:131 , SER L:132 , CSD L:133 , HOH L:244
BINDING SITE FOR RESIDUE 3CO L 301
10
BC1
SOFTWARE
VAL J:68 , ARG L:177 , HOH L:482 , HOH L:520 , HOH L:565 , HOH L:675 , HOH L:737 , HOH L:922 , HOH L:1049 , HOH L:2156 , HOH L:2429 , HOH L:2763
BINDING SITE FOR RESIDUE TLA L 4004
11
BC2
SOFTWARE
HOH J:785 , GLU L:83 , ASP L:84 , HOH L:1383 , HOH L:1475
BINDING SITE FOR RESIDUE FRU L 6001
12
BC3
SOFTWARE
HIS H:10 , LEU H:13 , GLY H:14 , HOH H:3316 , ARG L:157 , HOH L:466 , HOH L:1549 , HOH L:1618 , HOH L:1791 , HOH L:2365 , HOH L:2670
BINDING SITE FOR RESIDUE FRU L 6003
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2zzdL00 (L:24-239)
1b: CATH_2zzdC00 (C:23-239)
1c: CATH_2zzdI00 (I:23-239)
1d: CATH_2zzdF00 (F:23-240)
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(
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Nitrile Hydratase; Chain A
(34)
Homologous Superfamily
:
Nitrile Hydratase; Chain A
(34)
Thiobacillus thioparus. Organism_taxid: 931. Strain: thi115.
(1)
1a
2zzdL00
L:24-239
1b
2zzdC00
C:23-239
1c
2zzdI00
I:23-239
1d
2zzdF00
F:23-240
[
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Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_NHase_alpha_2zzdL01 (L:24-220)
1b: PFAM_NHase_alpha_2zzdL02 (L:24-220)
1c: PFAM_NHase_alpha_2zzdL03 (L:24-220)
1d: PFAM_NHase_alpha_2zzdL04 (L:24-220)
2a: PFAM_NHase_beta_2zzdJ01 (J:7-126)
2b: PFAM_NHase_beta_2zzdJ02 (J:7-126)
2c: PFAM_NHase_beta_2zzdJ03 (J:7-126)
2d: PFAM_NHase_beta_2zzdJ04 (J:7-126)
2e: PFAM_NHase_beta_2zzdK01 (K:44-148)
2f: PFAM_NHase_beta_2zzdK02 (K:44-148)
2g: PFAM_NHase_beta_2zzdK03 (K:44-148)
2h: PFAM_NHase_beta_2zzdK04 (K:44-148)
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Clans
(
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(
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Families
(
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(
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Organisms
(
)
(
)
Clan
:
no clan defined [family: NHase_alpha]
(12)
Family
:
NHase_alpha
(12)
Thiobacillus thioparus
(1)
1a
NHase_alpha-2zzdL01
L:24-220
1b
NHase_alpha-2zzdL02
L:24-220
1c
NHase_alpha-2zzdL03
L:24-220
1d
NHase_alpha-2zzdL04
L:24-220
Clan
:
no clan defined [family: NHase_beta]
(11)
Family
:
NHase_beta
(11)
Thiobacillus thioparus
(1)
2a
NHase_beta-2zzdJ01
J:7-126
2b
NHase_beta-2zzdJ02
J:7-126
2c
NHase_beta-2zzdJ03
J:7-126
2d
NHase_beta-2zzdJ04
J:7-126
2e
NHase_beta-2zzdK01
K:44-148
2f
NHase_beta-2zzdK02
K:44-148
2g
NHase_beta-2zzdK03
K:44-148
2h
NHase_beta-2zzdK04
K:44-148
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