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3ABR
Biol. Unit 1
Info
Asym.Unit (482 KB)
Biol.Unit 1, α-C (1.4 MB)
Biol.Unit 1 (1.4 MB)
Biol.Unit 2 (472 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ETHANOLAMINE AMMONIA-LYASE FROM ESCHERICHIA COLI COMPLEXED WITH CN-CBL (SUBSTRATE-FREE FORM)
Authors
:
N. Shibata
Date
:
21 Dec 09 (Deposition) - 02 Jun 10 (Release) - 19 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (3x)
Biol. Unit 2: A,B,C,D (1x)
Keywords
:
(Beta/Alpha)8 Fold, Cobalt, Lyase, Cobalamin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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)
Reference
:
N. Shibata, H. Tamagaki, N. Hieda, K. Akita, H. Komori, Y. Shomura, S. Terawaki, K. Mori, N. Yasuoka, Y. Higuchi, T. Toraya
Crystal Structures Of Ethanolamine Ammonia-Lyase Complexed With Coenzyme B12 Analogs And Substrates.
J. Biol. Chem. V. 285 26484 2010
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: COBALAMIN (B12a)
1b: COBALAMIN (B12b)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
3e: SODIUM ION (NAe)
3f: SODIUM ION (NAf)
3g: SODIUM ION (NAg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B12
6
Ligand/Ion
COBALAMIN
2
GOL
18
Ligand/Ion
GLYCEROL
3
NA
-1
Ligand/Ion
SODIUM ION
[
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Sites
(15, 15)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:272 , ALA A:273 , ILE A:278 , GLY A:280 , GLU A:281 , ASN A:282 , CYS A:283 , HOH A:976 , LYS C:115
BINDING SITE FOR RESIDUE GOL A 2001
02
AC2
SOFTWARE
LYS A:115 , GLY C:272 , ALA C:273 , GLY C:280 , GLU C:281 , ASN C:282 , CYS C:283 , HOH C:558
BINDING SITE FOR RESIDUE GOL A 2002
03
AC3
SOFTWARE
ASN A:148 , ARG A:277 , HOH A:466 , HOH A:711 , GLN C:87 , PHE C:112
BINDING SITE FOR RESIDUE GOL A 2006
04
AC4
SOFTWARE
SER A:295 , TYR A:334 , PRO B:137
BINDING SITE FOR RESIDUE NA A 3001
05
AC5
SOFTWARE
ILE A:235 , GLY A:238 , ALA A:239
BINDING SITE FOR RESIDUE NA A 3004
06
AC6
SOFTWARE
ASP A:398 , VAL B:75 , HOH B:348
BINDING SITE FOR RESIDUE NA A 3005
07
AC7
SOFTWARE
ASN A:193 , PRO A:194 , SER A:247 , GLU A:257 , PHE A:258 , SER A:295 , PHE A:329 , ILE A:330 , MET A:401 , LEU A:402 , HOH A:518 , HOH A:524 , ARG B:141 , ARG B:206 , VAL B:207 , LYS B:208 , GLU B:228 , ARG B:229 , TYR B:241 , GLU B:253 , ARG B:256 , CYS B:258 , SER B:260 , ASN B:261 , HOH B:307 , HOH B:313 , HOH B:320 , HOH B:322 , HOH B:533 , HOH B:872 , HOH B:895
BINDING SITE FOR RESIDUE B12 B 601
08
AC8
SOFTWARE
LEU B:96 , SER B:100 , HOH B:913 , VAL C:45 , HOH C:466
BINDING SITE FOR RESIDUE NA B 3002
09
AC9
SOFTWARE
ILE C:144 , LYS C:145 , LYS C:146 , THR C:150 , HOH C:665 , HOH C:898 , HOH C:936
BINDING SITE FOR RESIDUE GOL C 2003
10
BC1
SOFTWARE
HOH A:590 , HOH A:616 , VAL C:143 , LYS C:145 , ARG C:316 , GLY C:356 , HOH C:469 , HOH C:795
BINDING SITE FOR RESIDUE GOL C 2004
11
BC2
SOFTWARE
ARG C:60 , ASN C:61 , HOH C:943
BINDING SITE FOR RESIDUE GOL C 2005
12
BC3
SOFTWARE
ASP C:69
BINDING SITE FOR RESIDUE NA C 3007
13
BC4
SOFTWARE
PRO C:194 , LEU C:225 , PHE C:245 , SER C:247 , GLU C:257 , PHE C:258 , SER C:295 , PHE C:329 , ILE C:330 , MET C:401 , LEU C:402 , HOH C:492 , TYR D:133 , ARG D:141 , ARG D:206 , VAL D:207 , GLU D:228 , ARG D:229 , TYR D:241 , GLU D:253 , ARG D:256 , CYS D:258 , SER D:260 , HOH D:309 , HOH D:310 , HOH D:315 , HOH D:357 , HOH D:568 , HOH D:735
BINDING SITE FOR RESIDUE B12 D 601
14
BC5
SOFTWARE
SER D:170 , GLU D:228 , SER D:235 , SER D:237
BINDING SITE FOR RESIDUE NA D 3003
15
BC6
SOFTWARE
SER D:260 , ASN D:261
BINDING SITE FOR RESIDUE NA D 3006
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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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End label:
Sorry, no Info available
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_3abrA03 (A:142-453)
1b: CATH_3abrC03 (C:142-453)
2a: CATH_3abrA02 (A:55-141)
2b: CATH_3abrC02 (C:55-141)
3a: CATH_3abrA01 (A:1-54)
3b: CATH_3abrC01 (C:1-54)
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Classes
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(
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(
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Topologies
(
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(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Escherichia coli. Organism_taxid: 83333. Strain: k12.
(5)
1a
3abrA03
A:142-453
1b
3abrC03
C:142-453
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Annexin V; domain 1
(80)
Homologous Superfamily
:
lyase
(5)
Escherichia coli. Organism_taxid: 83333. Strain: k12.
(4)
2a
3abrA02
A:55-141
2b
3abrC02
C:55-141
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Ribosomal Protein L24e; Chain: T;
(92)
Homologous Superfamily
:
ethanolamine ammonia-lyase heavy chain domain like
(5)
Escherichia coli. Organism_taxid: 83333. Strain: k12.
(4)
3a
3abrA01
A:1-54
3b
3abrC01
C:1-54
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Chain D
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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Example Command
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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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Asym.Unit (482 KB)
Header - Asym.Unit
Biol.Unit 1 (1.4 MB)
Header - Biol.Unit 1
Biol.Unit 2 (472 KB)
Header - Biol.Unit 2
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