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3B1E
Biol. Unit 2
Info
Asym.Unit (303 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (150 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BETAC-S LYASE FROM STREPTOCOCCUS ANGINOSUS IN COMPLEX WITH L-SERINE: ALPHA-AMINOACRYLATE FORM
Authors
:
Y. Kezuka, Y. Yoshida, T. Nonaka
Date
:
29 Jun 11 (Deposition) - 27 Jun 12 (Release) - 10 May 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
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: 2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PH... (0JOa)
1b: 2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PH... (0JOb)
1c: 2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PH... (0JOc)
1d: 2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PH... (0JOd)
2a: ACETATE ION (ACTa)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
3c: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEc)
3d: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEd)
3e: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEe)
3f: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEf)
3g: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEg)
3h: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEh)
3i: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEi)
3j: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEj)
3k: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEk)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
0JO
2
Ligand/Ion
2-{[(E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}PROP-2-ENOICACID
2
ACT
1
Ligand/Ion
ACETATE ION
3
EPE
6
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
NA
-1
Ligand/Ion
SODIUM ION
[
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Sites
(15, 15)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC4 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
14: CC1 (SOFTWARE)
15: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
TYR A:60 , GLU A:268 , HOH A:854 , HOH A:1188 , TYR B:18 , TRP B:33 , VAL B:95 , TYR B:119 , HOH B:980 , EPE C:502 , HOH C:972
BINDING SITE FOR RESIDUE EPE A 501
02
AC3
SOFTWARE
PRO A:120 , PRO A:121 , ASP A:355 , HOH A:967 , HOH A:987 , HOH A:1012 , HOH A:1055 , HOH A:1064 , HOH A:1102 , EPE B:501 , ASP D:336 , ARG D:352
BINDING SITE FOR RESIDUE EPE A 502
03
AC4
SOFTWARE
ASP A:84 , LYS A:85 , GLU A:86 , HOH A:898 , GLN C:28
BINDING SITE FOR RESIDUE EPE A 503
04
AC8
SOFTWARE
ASP B:84 , LYS B:85 , GLU B:86 , HOH B:948 , HOH B:1139 , GLN D:28
BINDING SITE FOR RESIDUE EPE B 502
05
BC1
SOFTWARE
ILE C:34 , ALA C:35 , GLY C:93 , 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 , LYS C:234 , ARG C:365 , HOH C:803 , HOH C:844 , HOH C:867 , HOH C:886 , HOH C:899 , HOH C:1004 , HOH C:1067 , TYR D:60
BINDING SITE FOR RESIDUE P1T C 401
06
BC2
SOFTWARE
TYR C:60 , GLU C:268 , HOH C:832 , HOH C:1083 , HOH C:1115 , TYR D:18 , TRP D:33 , VAL D:95 , TYR D:119 , EPE D:502 , HOH D:859 , HOH D:1019
BINDING SITE FOR RESIDUE EPE C 501
07
BC3
SOFTWARE
EPE A:501 , PRO B:120 , PRO B:121 , ASP B:355 , HOH B:857 , HOH B:895 , HOH B:1055 , ASP C:336 , ARG C:352 , HOH C:972 , HOH C:1149
BINDING SITE FOR RESIDUE EPE C 502
08
BC4
SOFTWARE
ASP B:336 , ARG B:352 , PRO C:120 , PRO C:121 , ASP C:355 , HOH C:984 , HOH C:1014 , HOH C:1085 , EPE D:501
BINDING SITE FOR RESIDUE EPE C 503
09
BC5
SOFTWARE
HOH B:1042 , SER C:358 , HOH C:925 , HOH C:1076 , HOH C:1156
BINDING SITE FOR RESIDUE NA C 601
10
BC6
SOFTWARE
GLN C:47 , HIS C:50 , GLU C:54 , HOH C:926 , HIS D:50
BINDING SITE FOR RESIDUE ACT C 701
11
BC7
SOFTWARE
TYR C:60 , 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:849 , HOH D:859 , HOH D:865 , HOH D:887 , HOH D:905 , HOH D:908 , HOH D:996
BINDING SITE FOR RESIDUE P1T D 401
12
BC8
SOFTWARE
TYR C:18 , TRP C:33 , VAL C:95 , TYR C:119 , EPE C:503 , HOH C:803 , HOH C:984 , TYR D:60 , GLU D:268 , HOH D:934
BINDING SITE FOR RESIDUE EPE D 501
13
BC9
SOFTWARE
PHE A:339 , THR A:340 , EPE C:501 , PRO D:120 , PRO D:121 , ASP D:355 , HOH D:865 , HOH D:907 , HOH D:935 , HOH D:1004 , HOH D:1019 , HOH D:1052
BINDING SITE FOR RESIDUE EPE D 502
14
CC1
SOFTWARE
ASP D:84 , LYS D:85 , GLU D:86 , HOH D:986
BINDING SITE FOR RESIDUE EPE D 503
15
CC2
SOFTWARE
SER D:358 , HOH D:851 , HOH D:976 , HOH D:1003 , HOH D:1154 , HOH D:1155
BINDING SITE FOR RESIDUE NA D 601
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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)
Info
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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_d3b1ea_ (A:)
1b: SCOP_d3b1eb_ (B:)
1c: SCOP_d3b1ec_ (C:)
1d: SCOP_d3b1ed_ (D:)
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Protein Domains
(
)
(
)
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
d3b1ea_
A:
1b
d3b1eb_
B:
1c
d3b1ec_
C:
1d
d3b1ed_
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 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 (303 KB)
Header - Asym.Unit
Biol.Unit 1 (153 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
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