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2YF4
Asym. Unit
Info
Asym.Unit (458 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (154 KB)
Biol.Unit 3 (150 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DR2231, THE MAZG-LIKE PROTEIN FROM DEINOCOCCUS RADIODURANS, APO STRUCTURE
Authors
:
A. M. D. Goncalves, D. Desanctis, S. M. Mcsweeney
Date
:
01 Apr 11 (Deposition) - 06 Jul 11 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Keywords
:
Hydrolase, Dimeric Dutpase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. M. D. Goncalves, D. Desanctis, S. M. Mcsweeney
Structural And Functional Insights Into Dr2231 Protein, The Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase From Deinococcus Radiodurans.
J. Biol. Chem. V. 286 30691 2011
[
close entry info
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Hetero Components
(2, 41)
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)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
2a: SULFATE ION (SO4a)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
22
Ligand/Ion
GLYCEROL
2
SO4
19
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(41, 41)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:69 , GLY A:71 , GLN B:142 , GLY E:128
BINDING SITE FOR RESIDUE GOL A 1145
02
AC2
SOFTWARE
ARG A:135 , SO4 A:1150 , HOH A:2129 , PRO B:75 , PRO C:131 , HOH C:2146
BINDING SITE FOR RESIDUE GOL A 1146
03
AC3
SOFTWARE
PRO A:26 , GLU A:27 , ARG A:28 , HOH A:2035
BINDING SITE FOR RESIDUE GOL A 1147
04
AC4
SOFTWARE
HIS A:15 , THR A:25 , PRO A:26 , GLU A:27 , ASP A:92 , ILE A:96 , ASP A:97 , HOH A:2093
BINDING SITE FOR RESIDUE GOL A 1148
05
AC5
SOFTWARE
ARG A:19 , ARG A:38 , HOH A:2131 , HOH A:2132
BINDING SITE FOR RESIDUE SO4 A 1149
06
AC6
SOFTWARE
ALA A:132 , ASP A:133 , VAL A:134 , ARG A:135 , GOL A:1146 , HIS B:78
BINDING SITE FOR RESIDUE SO4 A 1150
07
AC7
SOFTWARE
ARG A:118 , LYS A:122
BINDING SITE FOR RESIDUE SO4 A 1151
08
AC8
SOFTWARE
ARG B:19 , HOH B:2119 , HOH B:2120 , HOH B:2121 , GLN C:62 , PRO D:34
BINDING SITE FOR RESIDUE GOL B 1145
09
AC9
SOFTWARE
PRO B:26 , GLU B:27 , ARG B:28 , HOH B:2038
BINDING SITE FOR RESIDUE GOL B 1146
10
BC1
SOFTWARE
LYS B:125 , HOH B:2123 , HIS F:57
BINDING SITE FOR RESIDUE GOL B 1147
11
BC2
SOFTWARE
HOH A:2128 , SER B:69 , ALA B:70 , GLY B:71 , ARG C:130
BINDING SITE FOR RESIDUE SO4 B 1148
12
BC3
SOFTWARE
ARG B:118 , LYS B:122
BINDING SITE FOR RESIDUE SO4 B 1149
13
BC4
SOFTWARE
HOH B:2124 , HOH B:2126 , ARG D:19
BINDING SITE FOR RESIDUE SO4 B 1150
14
BC5
SOFTWARE
HIS A:78 , ALA B:132 , VAL B:134 , ARG B:135
BINDING SITE FOR RESIDUE SO4 B 1151
15
BC6
SOFTWARE
ARG B:38 , HOH B:2127 , ARG C:19
BINDING SITE FOR RESIDUE SO4 B 1152
16
BC7
SOFTWARE
ARG C:13 , HOH C:2037 , HOH D:2100
BINDING SITE FOR RESIDUE GOL C 1145
17
BC8
SOFTWARE
GLU C:139 , HOH C:2151 , HOH C:2154 , HOH C:2160
BINDING SITE FOR RESIDUE GOL C 1146
18
BC9
SOFTWARE
ALA C:132 , ASP C:133 , VAL C:134 , ARG C:135 , HOH C:2161 , ALA D:74 , PRO D:75 , HIS D:78
BINDING SITE FOR RESIDUE GOL C 1147
19
CC1
SOFTWARE
SER C:69 , GLY C:71 , HOH C:2162 , GLU F:127 , GLY F:128 , GOL F:1147 , HOH F:2106
BINDING SITE FOR RESIDUE SO4 C 1148
20
CC2
SOFTWARE
ARG A:19 , HOH C:2164 , HOH C:2165
BINDING SITE FOR RESIDUE SO4 C 1149
21
CC3
SOFTWARE
ARG C:118 , LYS C:122
BINDING SITE FOR RESIDUE SO4 C 1150
22
CC4
SOFTWARE
ALA C:74 , PRO C:75 , HIS C:78 , ALA D:132 , ASP D:133 , VAL D:134 , ARG D:135 , HOH D:2138 , HOH D:2139 , HOH D:2140
BINDING SITE FOR RESIDUE GOL D 1145
23
CC5
SOFTWARE
HIS D:15 , GLU D:27 , ASP D:92 , GLY D:95 , ILE D:96 , ASP D:97 , HOH D:2141 , HOH D:2142
BINDING SITE FOR RESIDUE GOL D 1146
24
CC6
SOFTWARE
GLN C:142 , SER D:69 , ALA D:70 , GLY D:71
BINDING SITE FOR RESIDUE GOL D 1147
25
CC7
SOFTWARE
ARG D:118 , LYS D:122 , HIS E:57 , ALA E:60 , ARG E:61
BINDING SITE FOR RESIDUE GOL D 1148
26
CC8
SOFTWARE
LYS D:112 , GLN D:123 , LEU D:124 , LYS D:125 , HOH D:2145 , HOH D:2146 , HOH D:2150 , ARG E:61 , HOH E:2060
BINDING SITE FOR RESIDUE GOL D 1149
27
CC9
SOFTWARE
ARG D:117 , ARG D:118 , ALA D:119 , HOH D:2147 , HOH D:2148 , ARG E:117 , ALA F:20 , ILE F:21 , GLY F:22
BINDING SITE FOR RESIDUE GOL D 1150
28
DC1
SOFTWARE
GLU D:127 , GLY D:128 , SER E:69 , GLY E:71
BINDING SITE FOR RESIDUE SO4 D 1151
29
DC2
SOFTWARE
ARG D:135 , ARG F:135 , GOL F:1148
BINDING SITE FOR RESIDUE SO4 D 1152
30
DC3
SOFTWARE
LYS D:112 , LYS D:125 , HOH D:2149 , HOH D:2150
BINDING SITE FOR RESIDUE SO4 D 1153
31
DC4
SOFTWARE
GLU E:12 , HIS E:15 , SO4 E:1149 , HOH E:2096 , HOH E:2098
BINDING SITE FOR RESIDUE GOL E 1145
32
DC5
SOFTWARE
ARG D:19 , ARG E:38 , HOH E:2100 , HOH E:2101 , HOH E:2102
BINDING SITE FOR RESIDUE SO4 E 1146
33
DC6
SOFTWARE
ARG E:118 , LYS E:122
BINDING SITE FOR RESIDUE SO4 E 1147
34
DC7
SOFTWARE
ARG C:38 , LEU D:59 , ARG E:19 , HOH E:2103 , HOH E:2104 , HOH E:2105
BINDING SITE FOR RESIDUE SO4 E 1148
35
DC8
SOFTWARE
HIS E:15 , ARG E:19 , GOL E:1145 , HOH E:2106 , HOH E:2108
BINDING SITE FOR RESIDUE SO4 E 1149
36
DC9
SOFTWARE
HIS C:57 , ARG C:61 , ARG F:118 , LYS F:122 , HOH F:2105
BINDING SITE FOR RESIDUE GOL F 1145
37
EC1
SOFTWARE
HIS F:15 , PRO F:26 , GLU F:27 , ASP F:92 , ASP F:97
BINDING SITE FOR RESIDUE GOL F 1146
38
EC2
SOFTWARE
SO4 C:1148 , HOH C:2108 , LYS F:125 , TRP F:129 , HOH F:2106 , HOH F:2107 , HOH F:2108 , HOH F:2109
BINDING SITE FOR RESIDUE GOL F 1147
39
EC3
SOFTWARE
SO4 D:1152 , HIS E:78 , ALA F:132 , ASP F:133 , VAL F:134 , ARG F:135
BINDING SITE FOR RESIDUE GOL F 1148
40
EC4
SOFTWARE
HOH E:2095 , SER F:69 , GLY F:71
BINDING SITE FOR RESIDUE GOL F 1149
41
EC5
SOFTWARE
LYS F:112 , LYS F:122 , LYS F:125 , HOH F:2110 , HOH F:2111
BINDING SITE FOR RESIDUE SO4 F 1150
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_PRA_PH_2yf4F01 (F:14-109)
1b: PFAM_PRA_PH_2yf4F02 (F:14-109)
1c: PFAM_PRA_PH_2yf4F03 (F:14-109)
1d: PFAM_PRA_PH_2yf4F04 (F:14-109)
1e: PFAM_PRA_PH_2yf4F05 (F:14-109)
1f: PFAM_PRA_PH_2yf4F06 (F:14-109)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
MazG
(25)
Family
:
PRA-PH
(10)
Deinococcus radiodurans
(6)
1a
PRA-PH-2yf4F01
F:14-109
1b
PRA-PH-2yf4F02
F:14-109
1c
PRA-PH-2yf4F03
F:14-109
1d
PRA-PH-2yf4F04
F:14-109
1e
PRA-PH-2yf4F05
F:14-109
1f
PRA-PH-2yf4F06
F:14-109
[
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]
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