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3B1C
Biol. Unit 2
Info
Asym.Unit (294 KB)
Biol.Unit 1 (147 KB)
Biol.Unit 2 (147 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETAC-S LYASE FROM STREPTOCOCCUS ANGINOSUS: INTERNAL ALDIMINE FORM
Authors
:
Y. Kezuka, Y. Yoshida, T. Nonaka
Date
:
29 Jun 11 (Deposition) - 27 Jun 12 (Release) - 22 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.93
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kezuka, Y. Yoshida, T. Nonaka
Structural Insights Into Catalysis By Beta C-S Lyase From Streptococcus Anginosus
Proteins V. 80 2447 2012
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
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)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
3
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(17, 17)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC5 (SOFTWARE)
08: BC6 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC5 (SOFTWARE)
17: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
THR A:334 , ASP A:335 , GLU A:361 , HOH A:795 , SO4 D:502
BINDING SITE FOR RESIDUE GOL A 601
02
AC6
SOFTWARE
HIS A:259 , HOH A:870 , ALA C:337 , THR C:340 , HOH C:883 , HOH C:990
BINDING SITE FOR RESIDUE GOL A 604
03
AC9
SOFTWARE
ARG B:127 , LEU B:133 , HOH B:701 , HOH B:901 , HOH B:915 , HOH B:947 , HOH B:989 , GOL C:601
BINDING SITE FOR RESIDUE SO4 B 502
04
BC1
SOFTWARE
THR B:334 , ASP B:335 , GLU B:361 , HOH B:954 , ARG C:127
BINDING SITE FOR RESIDUE GOL B 601
05
BC3
SOFTWARE
ALA B:337 , THR B:340 , LEU B:341 , GLN B:345 , HOH B:855 , HOH B:861 , HOH B:912 , HOH B:1071 , HIS D:259
BINDING SITE FOR RESIDUE GOL B 603
06
BC4
SOFTWARE
GLY C:93 , VAL C:94 , VAL C:95 , TYR C:119 , CYS C:167 , ASN C:171 , ASP C:199 , ILE C:201 , HIS C:202 , LYS C:234 , HOH C:745 , HOH C:769 , HOH C:778 , HOH C:869 , TYR D:60
BINDING SITE FOR RESIDUE PLP C 401
07
BC5
SOFTWARE
ILE C:34 , ALA C:35 , TYR C:119 , ASN C:351 , ARG C:365 , HOH C:745 , HOH C:819 , HOH C:869 , HOH C:1053
BINDING SITE FOR RESIDUE SO4 C 501
08
BC6
SOFTWARE
ARG B:127 , SO4 B:502 , HOH B:947 , THR C:334 , ASP C:335 , GLU C:361
BINDING SITE FOR RESIDUE GOL C 601
09
BC7
SOFTWARE
GLU C:78 , LYS C:285 , LEU C:288 , LYS C:292 , HOH C:861 , HOH C:1043
BINDING SITE FOR RESIDUE GOL C 602
10
BC8
SOFTWARE
THR A:340 , LEU A:341 , HOH A:791 , HOH A:924 , HIS C:259 , HOH C:1020
BINDING SITE FOR RESIDUE GOL C 603
11
BC9
SOFTWARE
GLN C:28 , GLN C:345 , ALA C:346 , HOH C:1025
BINDING SITE FOR RESIDUE GOL C 604
12
CC1
SOFTWARE
TYR C:60 , HOH C:974 , GLY D:93 , VAL D:94 , VAL D:95 , TYR D:119 , CYS D:167 , ASN D:171 , ASP D:199 , ILE D:201 , HIS D:202 , LYS D:234 , HOH D:720 , HOH D:804 , HOH D:906
BINDING SITE FOR RESIDUE PLP D 401
13
CC2
SOFTWARE
ILE D:34 , ALA D:35 , TYR D:119 , ASN D:351 , ARG D:365 , HOH D:804 , HOH D:874 , HOH D:981
BINDING SITE FOR RESIDUE SO4 D 501
14
CC3
SOFTWARE
GOL A:601 , ARG D:127 , HOH D:733 , HOH D:858 , HOH D:984
BINDING SITE FOR RESIDUE SO4 D 502
15
CC4
SOFTWARE
ARG A:127 , THR D:334 , ASP D:335 , GLU D:361
BINDING SITE FOR RESIDUE GOL D 601
16
CC5
SOFTWARE
ASP D:73 , TRP D:74 , SER D:77 , GLU D:78 , LYS D:191 , TYR D:281 , LYS D:285 , HOH D:746 , HOH D:761 , HOH D:969
BINDING SITE FOR RESIDUE GOL D 602
17
CC6
SOFTWARE
ILE D:88 , VAL D:89 , PHE D:90 , HOH D:713 , HOH D:1018
BINDING SITE FOR RESIDUE GOL D 603
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3b1ca_ (A:)
1b: SCOP_d3b1cc_ (C:)
1c: SCOP_d3b1cd_ (D:)
1d: SCOP_d3b1cb_ (B:)
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Protein Domains
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Organisms
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(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
PLP-dependent transferases
(625)
Family
:
automated matches
(163)
Protein domain
:
automated matches
(163)
Streptococcus anginosus [TaxId: 1328]
(3)
1a
d3b1ca_
A:
1b
d3b1cc_
C:
1c
d3b1cd_
D:
1d
d3b1cb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
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Chain C
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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 (294 KB)
Header - Asym.Unit
Biol.Unit 1 (147 KB)
Header - Biol.Unit 1
Biol.Unit 2 (147 KB)
Header - Biol.Unit 2
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