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2R8Y
Asym. Unit
Info
Asym.Unit (456 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (120 KB)
Biol.Unit 3 (116 KB)
Biol.Unit 4 (116 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN A COMPLEX WITH CA
Authors
:
O. V. Tsodikov, P. Aggarwal, J. R. Rubin, J. A. Stuckey, R. W. Woodard, T. Biswas
Date
:
11 Sep 07 (Deposition) - 23 Sep 08 (Release) - 03 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Yrbi, Phosphatase, Divalent Metal, Ca, Had Superfamily, Kdo8-P, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Biswas, L. Yi, P. Aggarwal, J. Wu, J. R. Rubin, J. A. Stuckey, R. W. Woodard, O. V. Tsodikov
The Tail Of Kdsc: Conformational Changes Control The Activity Of A Haloacid Dehalogenase Superfamily Phosphatase.
J. Biol. Chem. V. 284 30594 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 32)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
2h: CHLORIDE ION (CLh)
2i: CHLORIDE ION (CLi)
2j: CHLORIDE ION (CLj)
2k: CHLORIDE ION (CLk)
2l: CHLORIDE ION (CLl)
2m: CHLORIDE ION (CLm)
2n: CHLORIDE ION (CLn)
2o: CHLORIDE ION (CLo)
2p: CHLORIDE ION (CLp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
16
Ligand/Ion
CALCIUM ION
2
CL
16
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:32 , ASP A:34 , ASP A:125 , HOH A:311 , HOH B:359 , HOH B:383
BINDING SITE FOR RESIDUE CA A 201
02
AC2
SOFTWARE
ASP B:32 , ASP B:34 , ASP B:125 , HOH B:332 , HOH C:305 , HOH C:340
BINDING SITE FOR RESIDUE CA B 202
03
AC3
SOFTWARE
ASP C:32 , ASP C:34 , ASP C:125 , HOH C:348 , HOH D:347
BINDING SITE FOR RESIDUE CA C 203
04
AC4
SOFTWARE
ASP D:32 , ASP D:34 , ASP D:125 , HOH D:334 , HOH D:373
BINDING SITE FOR RESIDUE CA D 204
05
AC5
SOFTWARE
ASP E:32 , ASP E:34 , ASP E:125 , HOH E:334
BINDING SITE FOR RESIDUE CA E 205
06
AC6
SOFTWARE
ASP F:32 , ASP F:34 , ASP F:125 , HOH F:325 , HOH F:344 , HOH G:388
BINDING SITE FOR RESIDUE CA F 206
07
AC7
SOFTWARE
ASP G:32 , ASP G:34 , ASP G:125 , HOH G:330 , HOH H:309 , HOH H:337
BINDING SITE FOR RESIDUE CA G 207
08
AC8
SOFTWARE
HOH E:329 , HOH E:372 , ASP H:32 , ASP H:34 , ASP H:125 , HOH H:317
BINDING SITE FOR RESIDUE CA H 208
09
AC9
SOFTWARE
ASP I:32 , ASP I:34 , ASP I:125 , HOH I:861
BINDING SITE FOR RESIDUE CA I 209
10
BC1
SOFTWARE
ASP J:32 , ASP J:34 , ASP J:125 , HOH J:417
BINDING SITE FOR RESIDUE CA J 210
11
BC2
SOFTWARE
ASP K:32 , ASP K:34 , ASP K:125
BINDING SITE FOR RESIDUE CA K 211
12
BC3
SOFTWARE
ASP L:32 , ASP L:34 , ASP L:125
BINDING SITE FOR RESIDUE CA L 212
13
BC4
SOFTWARE
ASP M:32 , ASP M:34 , ASP M:125 , HOH M:829
BINDING SITE FOR RESIDUE CA M 213
14
BC5
SOFTWARE
ASP N:32 , ASP N:34 , ASP N:125 , HOH N:331
BINDING SITE FOR RESIDUE CA N 214
15
BC6
SOFTWARE
ASP O:32 , ASP O:34 , ASP O:125 , HOH O:335
BINDING SITE FOR RESIDUE CA O 215
16
BC7
SOFTWARE
ASP P:32 , ASP P:34 , ASP P:125 , HOH P:938
BINDING SITE FOR RESIDUE CA P 216
17
BC8
SOFTWARE
ASP A:32 , GLY A:77 , LYS A:102 , HOH B:359 , HOH B:361
BINDING SITE FOR RESIDUE CL A 301
18
BC9
SOFTWARE
ASP B:32 , GLY B:77 , LYS B:102 , HOH C:340
BINDING SITE FOR RESIDUE CL B 302
19
CC1
SOFTWARE
ASP C:32 , GLY C:77 , LYS C:102 , HOH D:347
BINDING SITE FOR RESIDUE CL C 303
20
CC2
SOFTWARE
ASP D:32 , GLY D:77 , LYS D:102 , HOH D:373
BINDING SITE FOR RESIDUE CL D 304
21
CC3
SOFTWARE
LYS E:102
BINDING SITE FOR RESIDUE CL E 305
22
CC4
SOFTWARE
ASP F:32 , GLY F:77 , LYS F:102 , HOH G:388
BINDING SITE FOR RESIDUE CL F 306
23
CC5
SOFTWARE
ASP G:32 , GLY G:77 , LYS G:102 , HOH H:337
BINDING SITE FOR RESIDUE CL G 307
24
CC6
SOFTWARE
HOH E:329 , ASP H:32 , GLY H:77 , LYS H:102
BINDING SITE FOR RESIDUE CL H 308
25
CC7
SOFTWARE
ASP I:32 , GLY I:77 , LYS I:102
BINDING SITE FOR RESIDUE CL I 309
26
CC8
SOFTWARE
ASP J:32 , GLY J:77 , LYS J:102
BINDING SITE FOR RESIDUE CL J 310
27
CC9
SOFTWARE
ASP K:32 , GLY K:77 , LYS K:102
BINDING SITE FOR RESIDUE CL K 311
28
DC1
SOFTWARE
GLY L:77 , LYS L:102
BINDING SITE FOR RESIDUE CL L 312
29
DC2
SOFTWARE
ASP M:32 , GLY M:77 , LYS M:102
BINDING SITE FOR RESIDUE CL M 313
30
DC3
SOFTWARE
ASP N:32 , GLY N:77 , LYS N:102
BINDING SITE FOR RESIDUE CL N 314
31
DC4
SOFTWARE
ASP O:32 , GLY O:77 , LYS O:102
BINDING SITE FOR RESIDUE CL O 315
32
DC5
SOFTWARE
ASP P:32 , GLY P:77 , LYS P:102
BINDING SITE FOR RESIDUE CL P 316
[
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
[
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]
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
(1, 16)
Info
All SCOP Domains
1a: SCOP_d2r8ya_ (A:)
1b: SCOP_d2r8yb_ (B:)
1c: SCOP_d2r8yk_ (K:)
1d: SCOP_d2r8yl_ (L:)
1e: SCOP_d2r8ym_ (M:)
1f: SCOP_d2r8yn_ (N:)
1g: SCOP_d2r8yo_ (O:)
1h: SCOP_d2r8yp_ (P:)
1i: SCOP_d2r8yc_ (C:)
1j: SCOP_d2r8yd_ (D:)
1k: SCOP_d2r8ye_ (E:)
1l: SCOP_d2r8yf_ (F:)
1m: SCOP_d2r8yg_ (G:)
1n: SCOP_d2r8yh_ (H:)
1o: SCOP_d2r8yi_ (I:)
1p: SCOP_d2r8yj_ (J:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
automated matches
(99)
Protein domain
:
automated matches
(99)
Escherichia coli [TaxId: 562]
(4)
1a
d2r8ya_
A:
1b
d2r8yb_
B:
1c
d2r8yk_
K:
1d
d2r8yl_
L:
1e
d2r8ym_
M:
1f
d2r8yn_
N:
1g
d2r8yo_
O:
1h
d2r8yp_
P:
1i
d2r8yc_
C:
1j
d2r8yd_
D:
1k
d2r8ye_
E:
1l
d2r8yf_
F:
1m
d2r8yg_
G:
1n
d2r8yh_
H:
1o
d2r8yi_
I:
1p
d2r8yj_
J:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Hydrolase_3_2r8yP01 (P:88-167)
1b: PFAM_Hydrolase_3_2r8yP02 (P:88-167)
1c: PFAM_Hydrolase_3_2r8yP03 (P:88-167)
1d: PFAM_Hydrolase_3_2r8yP04 (P:88-167)
1e: PFAM_Hydrolase_3_2r8yP05 (P:88-167)
1f: PFAM_Hydrolase_3_2r8yP06 (P:88-167)
1g: PFAM_Hydrolase_3_2r8yP07 (P:88-167)
1h: PFAM_Hydrolase_3_2r8yP08 (P:88-167)
1i: PFAM_Hydrolase_3_2r8yP09 (P:88-167)
1j: PFAM_Hydrolase_3_2r8yP10 (P:88-167)
1k: PFAM_Hydrolase_3_2r8yP11 (P:88-167)
1l: PFAM_Hydrolase_3_2r8yP12 (P:88-167)
1m: PFAM_Hydrolase_3_2r8yP13 (P:88-167)
1n: PFAM_Hydrolase_3_2r8yP14 (P:88-167)
1o: PFAM_Hydrolase_3_2r8yP15 (P:88-167)
1p: PFAM_Hydrolase_3_2r8yP16 (P:88-167)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase_3
(28)
Escherichia coli O6
(4)
1a
Hydrolase_3-2r8yP01
P:88-167
1b
Hydrolase_3-2r8yP02
P:88-167
1c
Hydrolase_3-2r8yP03
P:88-167
1d
Hydrolase_3-2r8yP04
P:88-167
1e
Hydrolase_3-2r8yP05
P:88-167
1f
Hydrolase_3-2r8yP06
P:88-167
1g
Hydrolase_3-2r8yP07
P:88-167
1h
Hydrolase_3-2r8yP08
P:88-167
1i
Hydrolase_3-2r8yP09
P:88-167
1j
Hydrolase_3-2r8yP10
P:88-167
1k
Hydrolase_3-2r8yP11
P:88-167
1l
Hydrolase_3-2r8yP12
P:88-167
1m
Hydrolase_3-2r8yP13
P:88-167
1n
Hydrolase_3-2r8yP14
P:88-167
1o
Hydrolase_3-2r8yP15
P:88-167
1p
Hydrolase_3-2r8yP16
P:88-167
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Asym.Unit (456 KB)
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Biol.Unit 1 (121 KB)
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Biol.Unit 3 (116 KB)
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