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1VI9
Asym. Unit
Info
Asym.Unit (206 KB)
Biol.Unit 1 (101 KB)
Biol.Unit 2 (102 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PYRIDOXAMINE KINASE
Authors
:
Structural Genomix
Date
:
01 Dec 03 (Deposition) - 30 Dec 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.96
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Structural Genomics, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
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Hetero Components
(4, 42)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
2a: 3-SULFINOALANINE (CSDa)
2b: 3-SULFINOALANINE (CSDb)
2c: 3-SULFINOALANINE (CSDc)
2d: 3-SULFINOALANINE (CSDd)
3a: SELENOMETHIONINE (MSEa)
3aa: SELENOMETHIONINE (MSEaa)
3ab: SELENOMETHIONINE (MSEab)
3ac: SELENOMETHIONINE (MSEac)
3ad: SELENOMETHIONINE (MSEad)
3ae: SELENOMETHIONINE (MSEae)
3af: SELENOMETHIONINE (MSEaf)
3b: SELENOMETHIONINE (MSEb)
3c: SELENOMETHIONINE (MSEc)
3d: SELENOMETHIONINE (MSEd)
3e: SELENOMETHIONINE (MSEe)
3f: SELENOMETHIONINE (MSEf)
3g: SELENOMETHIONINE (MSEg)
3h: SELENOMETHIONINE (MSEh)
3i: SELENOMETHIONINE (MSEi)
3j: SELENOMETHIONINE (MSEj)
3k: SELENOMETHIONINE (MSEk)
3l: SELENOMETHIONINE (MSEl)
3m: SELENOMETHIONINE (MSEm)
3n: SELENOMETHIONINE (MSEn)
3o: SELENOMETHIONINE (MSEo)
3p: SELENOMETHIONINE (MSEp)
3q: SELENOMETHIONINE (MSEq)
3r: SELENOMETHIONINE (MSEr)
3s: SELENOMETHIONINE (MSEs)
3t: SELENOMETHIONINE (MSEt)
3u: SELENOMETHIONINE (MSEu)
3v: SELENOMETHIONINE (MSEv)
3w: SELENOMETHIONINE (MSEw)
3x: SELENOMETHIONINE (MSEx)
3y: SELENOMETHIONINE (MSEy)
3z: SELENOMETHIONINE (MSEz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
2
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CSD
4
Mod. Amino Acid
3-SULFINOALANINE
3
MSE
32
Mod. Amino Acid
SELENOMETHIONINE
4
SO4
4
Ligand/Ion
SULFATE ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:220 , GLY A:221 , VAL A:222 , GLY A:223 , ASP A:224 , HOH A:530
BINDING SITE FOR RESIDUE SO4 A 298
2
AC2
SOFTWARE
GLY B:221 , VAL B:222 , GLY B:223 , ASP B:224 , BME B:300 , HOH B:343 , HOH B:367 , HOH B:450 , HOH B:512 , HOH B:536
BINDING SITE FOR RESIDUE SO4 B 298
3
AC3
SOFTWARE
GLY C:221 , VAL C:222 , GLY C:223 , ASP C:224
BINDING SITE FOR RESIDUE SO4 C 298
4
AC4
SOFTWARE
GLY D:221 , VAL D:222 , GLY D:223 , ASP D:224 , BME D:300 , HOH D:337 , HOH D:520 , HOH D:523
BINDING SITE FOR RESIDUE SO4 D 298
5
AC5
SOFTWARE
CYS B:122 , ASP B:224 , SO4 B:298
BINDING SITE FOR RESIDUE BME B 300
6
AC6
SOFTWARE
TYR D:83 , CYS D:122 , VAL D:220 , ASP D:224 , SO4 D:298 , HOH D:357 , HOH D:523
BINDING SITE FOR RESIDUE BME D 300
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1vi9a_ (A:)
1b: SCOP_d1vi9b_ (B:)
1c: SCOP_d1vi9c_ (C:)
1d: SCOP_d1vi9d_ (D:)
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Classes
(
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(
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)
(
)
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)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribokinase-like
(226)
Superfamily
:
Ribokinase-like
(189)
Family
:
PfkB-like kinase
(20)
Protein domain
:
Pyridoxamine kinase
(2)
Escherichia coli [TaxId: 562]
(2)
1a
d1vi9a_
A:
1b
d1vi9b_
B:
1c
d1vi9c_
C:
1d
d1vi9d_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1vi9A00 (A:1-288)
1b: CATH_1vi9B00 (B:1-288)
1c: CATH_1vi9C00 (C:1-288)
1d: CATH_1vi9D00 (D:1-288)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase
(109)
Homologous Superfamily
:
[code=3.40.1190.20, no name defined]
(73)
Escherichia coli. Organism_taxid: 562.
(4)
1a
1vi9A00
A:1-288
1b
1vi9B00
B:1-288
1c
1vi9C00
C:1-288
1d
1vi9D00
D:1-288
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Chain D
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (206 KB)
Header - Asym.Unit
Biol.Unit 1 (101 KB)
Header - Biol.Unit 1
Biol.Unit 2 (102 KB)
Header - Biol.Unit 2
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