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2OOG
Asym. Unit
Info
Asym.Unit (307 KB)
Biol.Unit 1 (56 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (53 KB)
Biol.Unit 4 (56 KB)
Biol.Unit 5 (53 KB)
Biol.Unit 6 (53 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE FROM STAPHYLOCOCCUS AUREUS
Authors
:
Y. Patskovsky, E. Fedorov, R. Toro, J. M. Sauder, D. Smith, J. Freeman, M A. Powell, T. Gheyi, S. R. Wasserman, S. K. Burley, S. C. Almo, New York Research Center For Structural Genomics (Nysgxrc)
Date
:
25 Jan 07 (Deposition) - 06 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F
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)
Keywords
:
Phosphatase, Glycerophosphoryl Diester Phosphodiesterase, Structural Genomics, Protein Structure Initiative, Psi, New York Sgx Research Center For Structural Genomics, Nysgrc, Nysgxrc, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Patskovsky, J. M. Sauder, D. Smith, J. Freeman, M. Maletic, A. Powell, T. Gheyi, S. R. Wasserman, S. K. Burley, S. C. Almo
Crystal Structure Of Glycerophosphoryl Diester Phosphodiesterase From Staphylococcus Aureus
To Be Published
[
close entry info
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Hetero Components
(3, 51)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1aa: GLYCEROL (GOLaa)
1ab: GLYCEROL (GOLab)
1ac: GLYCEROL (GOLac)
1ad: GLYCEROL (GOLad)
1ae: GLYCEROL (GOLae)
1af: GLYCEROL (GOLaf)
1ag: GLYCEROL (GOLag)
1ah: GLYCEROL (GOLah)
1ai: GLYCEROL (GOLai)
1aj: GLYCEROL (GOLaj)
1ak: GLYCEROL (GOLak)
1al: GLYCEROL (GOLal)
1am: GLYCEROL (GOLam)
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)
1w: GLYCEROL (GOLw)
1x: GLYCEROL (GOLx)
1y: GLYCEROL (GOLy)
1z: GLYCEROL (GOLz)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
39
Ligand/Ion
GLYCEROL
2
SO4
6
Ligand/Ion
SULFATE ION
3
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
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Sites
(51, 51)
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)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:87 , ASP A:89 , GLU A:169 , GOL A:455 , HOH A:593 , HOH A:639
BINDING SITE FOR RESIDUE ZN A 403
02
AC2
SOFTWARE
HIS A:217 , ARG A:246
BINDING SITE FOR RESIDUE SO4 A 441
03
AC3
SOFTWARE
SER A:172 , SER A:209 , ASP A:210 , GLU A:211
BINDING SITE FOR RESIDUE SO4 A 442
04
AC4
SOFTWARE
HIS A:191 , ASN A:194
BINDING SITE FOR RESIDUE SO4 A 445
05
AC5
SOFTWARE
GLU B:87 , ASP B:89 , GLU B:169 , GOL B:452 , HOH B:642 , HOH B:652
BINDING SITE FOR RESIDUE ZN B 401
06
AC6
SOFTWARE
SER B:172 , SER B:209 , ASP B:210 , GLU B:211 , HOH B:517
BINDING SITE FOR RESIDUE SO4 B 443
07
AC7
SOFTWARE
GLU C:87 , ASP C:89 , GLU C:169 , GOL C:451 , HOH C:484
BINDING SITE FOR RESIDUE ZN C 406
08
AC8
SOFTWARE
SER C:172 , SER C:209 , ASP C:210 , GLU C:211 , HOH C:508 , HOH C:509
BINDING SITE FOR RESIDUE SO4 C 446
09
AC9
SOFTWARE
GLU D:87 , ASP D:89 , GLU D:169 , GOL D:453 , HOH D:549 , HOH D:656
BINDING SITE FOR RESIDUE ZN D 405
10
BC1
SOFTWARE
SER D:209 , ASP D:210 , GLU D:211
BINDING SITE FOR RESIDUE SO4 D 444
11
BC2
SOFTWARE
GLU E:87 , ASP E:89 , GLU E:169 , GOL E:454 , HOH E:512 , HOH E:534
BINDING SITE FOR RESIDUE ZN E 404
12
BC3
SOFTWARE
GLU F:87 , ASP F:89 , GLU F:169 , GOL F:456 , HOH F:512 , HOH F:554
BINDING SITE FOR RESIDUE ZN F 402
13
BC4
SOFTWARE
HIS A:59 , GLU A:87 , GLU A:169 , GLN A:206 , ZN A:403 , HOH A:650
BINDING SITE FOR RESIDUE GOL A 455
14
BC5
SOFTWARE
GLN A:72 , ASP A:75
BINDING SITE FOR RESIDUE GOL A 470
15
BC6
SOFTWARE
ASP A:154 , GLU A:158 , LYS A:189 , GOL A:487 , HOH A:686
BINDING SITE FOR RESIDUE GOL A 489
16
BC7
SOFTWARE
LYS A:76 , ARG A:142 , HOH A:530 , GLU F:158 , ARG F:159
BINDING SITE FOR RESIDUE GOL A 475
17
BC8
SOFTWARE
GLU A:80 , ARG A:142 , HOH A:654
BINDING SITE FOR RESIDUE GOL A 476
18
BC9
SOFTWARE
LYS A:189 , HIS A:191 , GOL A:489
BINDING SITE FOR RESIDUE GOL A 487
19
CC1
SOFTWARE
HIS B:59 , GLU B:87 , GLU B:169 , GLN B:206 , PHE B:297 , ZN B:401 , HOH B:598 , HOH B:652
BINDING SITE FOR RESIDUE GOL B 452
20
CC2
SOFTWARE
ASP B:75 , HIS B:78 , ASN B:79 , ARG B:159 , TYR B:160 , ARG D:142
BINDING SITE FOR RESIDUE GOL B 458
21
CC3
SOFTWARE
ARG B:142 , ALA B:143 , SER B:144
BINDING SITE FOR RESIDUE GOL B 461
22
CC4
SOFTWARE
GLU B:80 , LEU B:81 , LYS B:305 , HOH B:539
BINDING SITE FOR RESIDUE GOL B 469
23
CC5
SOFTWARE
GLN B:235 , GLN B:236
BINDING SITE FOR RESIDUE GOL B 472
24
CC6
SOFTWARE
ASN B:238 , ASP B:239 , GLN B:240 , HOH B:562
BINDING SITE FOR RESIDUE GOL B 473
25
CC7
SOFTWARE
ASN B:163 , ASN B:196 , LYS B:197 , ASN B:200 , HIS B:202 , LYS D:309
BINDING SITE FOR RESIDUE GOL B 477
26
CC8
SOFTWARE
HIS B:191 , ASN B:194 , HOH B:546 , HOH B:558 , HOH B:655
BINDING SITE FOR RESIDUE GOL B 478
27
CC9
SOFTWARE
GLU B:158 , HIS B:190 , HIS B:191 , HOH B:569
BINDING SITE FOR RESIDUE GOL B 479
28
DC1
SOFTWARE
HIS B:217 , ARG B:246 , SER B:247
BINDING SITE FOR RESIDUE GOL B 480
29
DC2
SOFTWARE
HIS C:59 , GLU C:87 , GLU C:169 , GLN C:206 , LEU C:228 , TYR C:277 , PHE C:297 , ZN C:406 , HOH C:485 , HOH C:559
BINDING SITE FOR RESIDUE GOL C 451
30
DC3
SOFTWARE
HIS C:97 , HOH C:542 , GOL D:481
BINDING SITE FOR RESIDUE GOL C 482
31
DC4
SOFTWARE
HIS D:59 , GLU D:87 , GLU D:169 , GLN D:206 , PHE D:297 , ZN D:405 , HOH D:602 , HOH D:656 , HOH D:664
BINDING SITE FOR RESIDUE GOL D 453
32
DC5
SOFTWARE
LYS B:305 , HOH B:640 , HOH B:657 , ASN D:51 , GOL D:484 , HOH D:594
BINDING SITE FOR RESIDUE GOL D 462
33
DC6
SOFTWARE
LYS B:309 , ASN D:196 , LYS D:197 , ASN D:200 , HIS D:202
BINDING SITE FOR RESIDUE GOL D 463
34
DC7
SOFTWARE
GLN D:219 , ASN D:220 , LYS D:221
BINDING SITE FOR RESIDUE GOL D 466
35
DC8
SOFTWARE
THR D:152 , GLU D:155
BINDING SITE FOR RESIDUE GOL D 468
36
DC9
SOFTWARE
ARG B:159 , ASN D:134 , ALA D:141 , LYS D:146 , HOH D:531 , HOH D:574
BINDING SITE FOR RESIDUE GOL D 471
37
EC1
SOFTWARE
LYS C:189 , GOL C:482 , HOH C:542 , HOH C:548 , LYS D:215 , ARG D:218 , GLN D:219
BINDING SITE FOR RESIDUE GOL D 481
38
EC2
SOFTWARE
HIS D:78 , ASN D:79 , LYS D:82 , HOH D:572
BINDING SITE FOR RESIDUE GOL D 483
39
EC3
SOFTWARE
THR D:50 , GLU D:52 , SER D:84 , ASN D:165 , GOL D:462 , HOH D:581
BINDING SITE FOR RESIDUE GOL D 484
40
EC4
SOFTWARE
HIS E:59 , GLN E:206 , PHE E:208 , TYR E:277 , PHE E:297 , ZN E:404 , HOH E:534
BINDING SITE FOR RESIDUE GOL E 454
41
EC5
SOFTWARE
GLY E:96 , HIS E:97 , LEU E:98 , GLN E:182 , LYS F:215 , GOL F:459
BINDING SITE FOR RESIDUE GOL E 465
42
EC6
SOFTWARE
LYS E:215 , ARG E:218 , LYS F:189
BINDING SITE FOR RESIDUE GOL E 467
43
EC7
SOFTWARE
GLU E:281 , LYS E:282 , LYS E:303
BINDING SITE FOR RESIDUE GOL E 474
44
EC8
SOFTWARE
ARG E:142 , ALA E:143 , SER E:144 , ARG F:142 , ALA F:143
BINDING SITE FOR RESIDUE GOL E 485
45
EC9
SOFTWARE
HIS F:59 , GLU F:87 , GLU F:169 , GLN F:206 , TYR F:277 , PHE F:297 , ZN F:402 , HOH F:512
BINDING SITE FOR RESIDUE GOL F 456
46
FC1
SOFTWARE
HOH A:654 , ASP F:75 , HIS F:78 , ASN F:79 , ARG F:159 , TYR F:160
BINDING SITE FOR RESIDUE GOL F 457
47
FC2
SOFTWARE
GOL E:465 , ARG F:218 , HOH F:497
BINDING SITE FOR RESIDUE GOL F 459
48
FC3
SOFTWARE
LYS F:188 , HIS F:191 , ASN F:194 , HOH F:555
BINDING SITE FOR RESIDUE GOL F 460
49
FC4
SOFTWARE
HOH A:530 , GLU F:158 , LYS F:189 , HIS F:190 , HIS F:191
BINDING SITE FOR RESIDUE GOL F 464
50
FC5
SOFTWARE
ARG F:246 , HOH F:526 , HOH F:572
BINDING SITE FOR RESIDUE GOL F 486
51
FC6
SOFTWARE
SER F:172 , PHE F:208 , SER F:209 , ASP F:210 , GLU F:211
BINDING SITE FOR RESIDUE GOL F 488
[
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:
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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, 6)
Info
All SCOP Domains
1a: SCOP_d2ooga_ (A:)
1b: SCOP_d2oogb_ (B:)
1c: SCOP_d2oogc_ (C:)
1d: SCOP_d2oogd_ (D:)
1e: SCOP_d2ooge_ (E:)
1f: SCOP_d2oogf_ (F:)
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Classes
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Superfamilies
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Families
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLC-like phosphodiesterases
(46)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Staphylococcus aureus [TaxId: 158879]
(2)
1a
d2ooga_
A:
1b
d2oogb_
B:
1c
d2oogc_
C:
1d
d2oogd_
D:
1e
d2ooge_
E:
1f
d2oogf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2oogD00 (D:44-311)
1b: CATH_2oogA00 (A:44-310)
1c: CATH_2oogB00 (B:44-310)
1d: CATH_2oogC00 (C:44-310)
1e: CATH_2oogE00 (E:44-310)
1f: CATH_2oogF00 (F:44-310)
View:
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Classes
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Architectures
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphatidylinositol (PI) phosphodiesterase
(37)
Aureus n315 (Staphylococcus aureus subsp)
(2)
1a
2oogD00
D:44-311
1b
2oogA00
A:44-310
1c
2oogB00
B:44-310
1d
2oogC00
C:44-310
1e
2oogE00
E:44-310
1f
2oogF00
F:44-310
[
close CATH info
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Pfam Domains
(0, 0)
Info
all PFAM domains
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