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3B1D
Biol. Unit 2
Info
Asym.Unit (302 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETAC-S LYASE FROM STREPTOCOCCUS ANGINOSUS IN COMPLEX WITH L-SERINE: EXTERNAL 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
:
1.66
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
)
[
close entry info
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
1b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
1c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
1d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
1e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
1f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
1g: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEg)
1h: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEh)
1i: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEi)
1j: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEj)
1k: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEk)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
3a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
3b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
4a: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXY... (PLSa)
4b: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXY... (PLSb)
4c: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXY... (PLSc)
4d: [3-HYDROXY-2-METHYL-5-PHOSPHONOOXY... (PLSd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EPE
6
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2
NA
-1
Ligand/Ion
SODIUM ION
3
PLP
1
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
4
PLS
2
Ligand/Ion
[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
[
close Hetero Component info
]
Sites
(14, 14)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: BC2 (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)
View:
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No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
TYR A:60 , GLU A:268 , HOH A:1041 , TYR B:18 , TRP B:33 , TYR B:119 , PLS B:501 , HOH B:1184 , HOH B:1201 , EPE C:602
BINDING SITE FOR RESIDUE EPE A 601
02
AC4
SOFTWARE
PRO A:120 , PRO A:121 , ASP A:355 , HOH A:1035 , HOH A:1079 , EPE B:601 , ASP D:336 , ARG D:352
BINDING SITE FOR RESIDUE EPE A 602
03
AC5
SOFTWARE
ASP A:84 , LYS A:85 , GLU A:86 , HOH A:940 , HOH A:1200 , GLN C:28
BINDING SITE FOR RESIDUE EPE A 603
04
BC2
SOFTWARE
VAL C:94 , VAL C:95 , PRO C:96 , TYR C:119 , CYS C:167 , ASN C:171 , ASP C:199 , ILE C:201 , HIS C:202 , HOH C:852 , HOH C:900 , HOH C:1139 , HOH C:1171 , TYR D:60
BINDING SITE FOR RESIDUE PLP C 401
05
BC3
SOFTWARE
ILE C:34 , ALA C:35 , 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 , ARG C:365 , HOH C:852 , HOH C:900 , HOH C:911 , HOH C:933 , HOH C:1139 , HOH C:1171 , TYR D:60 , EPE D:601
BINDING SITE FOR RESIDUE PLS C 501
06
BC4
SOFTWARE
TYR C:60 , GLU C:268 , HOH C:877 , TYR D:18 , TRP D:33 , VAL D:95 , TYR D:119 , PLS D:501 , EPE D:602 , HOH D:1037 , HOH D:1144
BINDING SITE FOR RESIDUE EPE C 601
07
BC5
SOFTWARE
EPE A:601 , PRO B:120 , PRO B:121 , HOH B:849 , HOH B:927 , HOH B:1100 , HOH B:1201 , HOH C:1040
BINDING SITE FOR RESIDUE EPE C 602
08
BC6
SOFTWARE
PRO C:120 , PRO C:121 , HOH C:911 , HOH C:1068 , HOH C:1097 , HOH C:1129 , EPE D:601
BINDING SITE FOR RESIDUE EPE C 603
09
BC7
SOFTWARE
SER C:358 , HOH C:923 , HOH C:949 , HOH C:1058 , HOH C:1114
BINDING SITE FOR RESIDUE NA C 701
10
BC8
SOFTWARE
TYR C:60 , EPE C:601 , ILE D:34 , ALA D:35 , 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 , ARG D:365 , HOH D:828 , HOH D:851 , HOH D:907 , HOH D:1037 , HOH D:1144
BINDING SITE FOR RESIDUE PLS D 501
11
BC9
SOFTWARE
TYR C:18 , TRP C:33 , VAL C:95 , TYR C:119 , PLS C:501 , EPE C:603 , HOH C:1097 , HOH C:1129 , HOH C:1139 , TYR D:60 , GLU D:268 , HOH D:927
BINDING SITE FOR RESIDUE EPE D 601
12
CC1
SOFTWARE
ASP A:336 , PHE A:339 , EPE C:601 , PRO D:120 , PRO D:121 , ASP D:355 , HOH D:989 , HOH D:1039 , HOH D:1063 , HOH D:1067 , HOH D:1106 , HOH D:1144
BINDING SITE FOR RESIDUE EPE D 602
13
CC2
SOFTWARE
ASP D:84 , LYS D:85 , GLU D:86 , HOH D:965
BINDING SITE FOR RESIDUE EPE D 603
14
CC3
SOFTWARE
SER D:358 , HOH D:827 , HOH D:939 , HOH D:964 , HOH D:966 , HOH D:1017
BINDING SITE FOR RESIDUE NA D 701
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
Info
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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_d3b1da_ (A:)
1b: SCOP_d3b1db_ (B:)
1c: SCOP_d3b1dc_ (C:)
1d: SCOP_d3b1dd_ (D:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
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
d3b1da_
A:
1b
d3b1db_
B:
1c
d3b1dc_
C:
1d
d3b1dd_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
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Asymmetric Unit 1
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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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set fontsize 20
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Show PDB file:
Asym.Unit (302 KB)
Header - Asym.Unit
Biol.Unit 1 (151 KB)
Header - Biol.Unit 1
Biol.Unit 2 (151 KB)
Header - Biol.Unit 2
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