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3JYF
Biol. Unit 3
Info
Asym.Unit (127 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (122 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF A 2,3-CYCLIC NUCLEOTIDE 2-PHOSPHODIESTERASE/3-NUCLEOTIDASE BIFUNCTIONAL PERIPLASMIC PRECURSOR PROTEIN FROM KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE MGH 78578
Authors
:
Y. Fan, L. Volkart, G. Cobb, A. Joachimiak, Midwest Center For Struc Genomics (Mcsg)
Date
:
21 Sep 09 (Deposition) - 29 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A (2x)
Keywords
:
Apc63187. 2, Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578, 2, 3- Cyclic Nucleotide 2-Phosphodiesterase, 3-Nucleotidase, Bifunctional Periplasmic Precursor Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Metal-Binding, Nucleotide-Binding, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Fan, L. Volkart, G. Cobb, A. Joachimiak
The Crystal Structure Of A 2, 3-Cyclic Nucleotide 2-Phosphodiesterase/3-Nucleotidase Bifunctional Periplasmic Precursor Protein From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
To Be Published
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Hetero Components
(4, 44)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
6a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
2
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
GOL
12
Ligand/Ion
GLYCEROL
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
4
MSE
24
Mod. Amino Acid
SELENOMETHIONINE
5
SO4
6
Ligand/Ion
SULFATE ION
6
TAM
-1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:16 , HIS A:18 , ASP A:61 , HIS A:244 , MN A:342 , HOH A:517
BINDING SITE FOR RESIDUE MN A 340
02
AC2
SOFTWARE
ASP A:61 , ASN A:101 , HIS A:102 , ASN A:105 , TRP A:172 , HIS A:242 , MN A:342 , GOL A:350 , HOH A:357 , HOH A:495 , HOH A:517 , HOH A:625 , HOH A:628 , HOH A:633
BINDING SITE FOR RESIDUE EPE A 341
03
AC3
SOFTWARE
ASP A:61 , ASN A:101 , HIS A:210 , HIS A:242 , MN A:340 , EPE A:341
BINDING SITE FOR RESIDUE MN A 342
04
AC4
SOFTWARE
PRO A:195 , GLU A:196 , LYS A:200 , HOH A:395
BINDING SITE FOR RESIDUE GOL A 343
05
AC5
SOFTWARE
LYS A:78 , GLU A:79 , LYS A:113
BINDING SITE FOR RESIDUE GOL A 344
06
AC6
SOFTWARE
ARG A:10 , VAL A:51 , ASP A:284 , LYS A:300 , HOH A:544
BINDING SITE FOR RESIDUE GOL A 345
07
AC7
SOFTWARE
ARG A:48 , ASN A:93 , HOH A:482 , HOH A:521
BINDING SITE FOR RESIDUE GOL A 346
08
AC8
SOFTWARE
LYS A:134 , ARG A:191 , GLN A:231 , PRO A:233 , HOH A:538
BINDING SITE FOR RESIDUE SO4 A 347
09
AC9
SOFTWARE
LYS A:256 , GLY A:257 , HOH A:491 , HOH A:518 , LYS B:256
BINDING SITE FOR RESIDUE SO4 A 348
10
BC1
SOFTWARE
ARG A:334
BINDING SITE FOR RESIDUE SO4 A 349
11
BC2
SOFTWARE
GLN A:64 , HIS A:102 , EPE A:341 , HOH A:486 , HOH A:628
BINDING SITE FOR RESIDUE GOL A 350
12
BC3
SOFTWARE
GLY A:107 , LEU A:108 , ASP A:109 , HOH A:361
BINDING SITE FOR RESIDUE GOL A 351
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3jyfB00 (B:4-338)
1b: CATH_3jyfA00 (A:4-339)
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Class
:
Alpha Beta
(26913)
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Purple Acid Phosphatase; chain A, domain 2
(87)
Homologous Superfamily
:
[code=3.60.21.10, no name defined]
(83)
Pneumoniae mgh 78578 (Klebsiella pneumoniae subsp)
(1)
1a
3jyfB00
B:4-338
1b
3jyfA00
A:4-339
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Metallophos_3jyfB01 (B:9-246)
1b: PFAM_Metallophos_3jyfB02 (B:9-246)
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Organisms
(
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(
)
Clan
:
Calcineurin
(56)
Family
:
Metallophos
(45)
Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
(1)
1a
Metallophos-3jyfB01
B:9-246
1b
Metallophos-3jyfB02
B:9-246
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (127 KB)
Header - Asym.Unit
Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (122 KB)
Header - Biol.Unit 3
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