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1ZCC
Asym. Unit
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Asym.Unit (227 KB)
Biol.Unit 1 (221 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM AGROBACTERIUM TUMEFACIENS STR.C58
Authors
:
N. R. Krishnamurthy, D. Kumaran, S. Swaminathan, S. K. Burley, New Yor Research Center For Structural Genomics (Nysgxrc)
Date
:
11 Apr 05 (Deposition) - 03 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Nysgxrc, T2047, Glycerophosphodiester Phosphodiesterase, Agrobacterium Tumefaciens Str. C58, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Hydrolase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
K. N. Rao, J. B. Bonanno, S. K. Burley, S. Swaminathan
Crystal Structure Of Glycerophosphodiester Phosphodiesteras From Agrobacterium Tumefaciens By Sad With A Large Asymmetric Unit.
Proteins V. 65 514 2006
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Hetero Components
(2, 12)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
SO4
6
Ligand/Ion
SULFATE ION
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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
TYR A:106 , GLU A:108 , MET A:153 , GLU A:175 , SO4 A:4770
BINDING SITE FOR RESIDUE ACT A 801
02
AC2
SOFTWARE
HIS A:7 , ARG A:8 , HIS A:49 , GLU A:108 , PHE A:135 , ACT A:801
BINDING SITE FOR RESIDUE SO4 A 4770
03
AC3
SOFTWARE
TYR B:106 , MET B:153 , GLU B:175 , SO4 B:4771 , HOH B:4789
BINDING SITE FOR RESIDUE ACT B 802
04
AC4
SOFTWARE
HIS B:7 , ARG B:8 , HIS B:49 , GLU B:108 , ACT B:802
BINDING SITE FOR RESIDUE SO4 B 4771
05
AC5
SOFTWARE
TYR C:106 , GLU C:108 , MET C:153 , GLU C:175 , SO4 C:4772
BINDING SITE FOR RESIDUE ACT C 803
06
AC6
SOFTWARE
HIS C:7 , ARG C:8 , HIS C:49 , ACT C:803
BINDING SITE FOR RESIDUE SO4 C 4772
07
AC7
SOFTWARE
TYR D:106 , GLU D:108 , GLU D:175 , ASN D:221
BINDING SITE FOR RESIDUE ACT D 804
08
AC8
SOFTWARE
HIS D:7 , ARG D:8 , HIS D:49 , GLU D:108 , LYS D:110
BINDING SITE FOR RESIDUE SO4 D 4773
09
AC9
SOFTWARE
GLU E:34 , TYR E:106 , GLU E:108 , GLU E:175 , ASN E:221 , SO4 E:4774
BINDING SITE FOR RESIDUE ACT E 805
10
BC1
SOFTWARE
HIS E:7 , ARG E:8 , HIS E:49 , ACT E:805
BINDING SITE FOR RESIDUE SO4 E 4774
11
BC2
SOFTWARE
GLU F:34 , TYR F:106 , GLU F:108 , MET F:153 , GLU F:175 , ASN F:221 , SO4 F:4775
BINDING SITE FOR RESIDUE ACT F 806
12
BC3
SOFTWARE
HIS F:7 , ARG F:8 , TYR F:200 , ACT F:806
BINDING SITE FOR RESIDUE SO4 F 4775
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1zccb_ (B:)
1b: SCOP_d1zccc_ (C:)
1c: SCOP_d1zccd_ (D:)
1d: SCOP_d1zcce_ (E:)
1e: SCOP_d1zccf_ (F:)
2a: SCOP_d1zcca1 (A:1-240)
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Protein Domains
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Organisms
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLC-like phosphodiesterases
(46)
Family
:
Glycerophosphoryl diester phosphodiesterase
(7)
Protein domain
:
automated matches
(2)
Agrobacterium tumefaciens [TaxId: 176299]
(1)
1a
d1zccb_
B:
1b
d1zccc_
C:
1c
d1zccd_
D:
1d
d1zcce_
E:
1e
d1zccf_
F:
Protein domain
:
Glycerophosphodiester phosphodiesterase UgpQ
(1)
Agrobacterium tumefaciens [TaxId: 358]
(1)
2a
d1zcca1
A:1-240
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CATH Domains
(0, 0)
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Pfam Domains
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Asymmetric Unit 1
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