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1EGV
Asym. Unit
Info
Asym.Unit (323 KB)
Biol.Unit 1 (314 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE DIOL DEHYDRATASE-ADENINYLPENTYLCOBALAMIN COMPLEX FROM KLEBSELLA OXYTOCA UNDER THE ILLUMINATED CONDITION.
Authors
:
J. Masuda, N. Shibata, T. Toraya, Y. Morimoto, N. Yasuoka
Date
:
17 Feb 00 (Deposition) - 21 Feb 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,E,G,L,M
Biol. Unit 1: A,B,E,G,L,M (1x)
Keywords
:
Coenzyme B12, Propanediol, Potassium Ion, Tim Barrel, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Masuda, N. Shibata, Y. Morimoto, T. Toraya, N. Yasuoka
How A Protein Generates A Catalytic Radical From Coenzyme B(12): X-Ray Structure Of A Diol-Dehydratase-Adeninylpentylcobalamin Complex.
Structure Fold. Des. V. 8 775 2000
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN (COYa)
1b: CO-(ADENIN-9-YL-PENTYL)-COBALAMIN (COYb)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
3a: S-1,2-PROPANEDIOL (PGOa)
3b: S-1,2-PROPANEDIOL (PGOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COY
2
Ligand/Ion
CO-(ADENIN-9-YL-PENTYL)-COBALAMIN
2
K
4
Ligand/Ion
POTASSIUM ION
3
PGO
2
Ligand/Ion
S-1,2-PROPANEDIOL
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:141 , GLU A:170 , GLU A:221 , GLN A:296 , SER A:362 , PGO A:602
BINDING SITE FOR RESIDUE K A 603
2
AC2
SOFTWARE
GLY A:261 , SER A:264 , GLU A:265 , GLU A:280 , CYS A:283 , HOH A:625 , HOH A:727
BINDING SITE FOR RESIDUE K A 604
3
AC3
SOFTWARE
GLN L:141 , GLU L:170 , GLU L:221 , GLN L:296 , SER L:362 , PGO L:602
BINDING SITE FOR RESIDUE K L 603
4
AC4
SOFTWARE
GLY L:261 , SER L:264 , GLU L:265 , GLU L:280 , CYS L:283 , HOH L:606 , HOH L:624
BINDING SITE FOR RESIDUE K L 604
5
AC5
SOFTWARE
THR A:172 , VAL A:173 , GLU A:205 , THR A:222 , SER A:224 , VAL A:225 , ASP A:234 , THR A:259 , SER A:260 , GLY A:261 , GLN A:267 , MET A:268 , SER A:299 , VAL A:300 , SER A:301 , GLN A:336 , MET A:373 , PHE A:374 , HOH A:623 , HOH A:625 , HOH A:639 , HOH A:713 , HOH A:753 , HOH A:783 , HOH A:844 , HOH A:1113 , ASP B:112 , LYS B:135 , THR B:137 , LEU B:148 , ASN B:150 , LEU B:153 , PRO B:155 , GLN B:156 , ALA B:157 , ARG B:193 , TYR B:196 , SER B:200 , HOH B:234
BINDING SITE FOR RESIDUE COY A 601
6
AC6
SOFTWARE
HIS A:143 , GLU A:170 , GLU A:221 , THR A:222 , GLN A:296 , ASP A:335 , GLN A:336 , SER A:362 , K A:603
BINDING SITE FOR RESIDUE PGO A 602
7
AC7
SOFTWARE
ASP E:112 , VAL E:113 , LYS E:135 , THR E:137 , LEU E:148 , ASN E:150 , LEU E:153 , PRO E:155 , GLN E:156 , ALA E:157 , ARG E:193 , TYR E:196 , GLN E:197 , SER E:200 , HOH E:229 , HOH E:230 , HOH E:266 , THR L:172 , VAL L:173 , GLU L:205 , THR L:222 , SER L:224 , ASP L:234 , THR L:259 , SER L:260 , GLY L:261 , GLN L:267 , MET L:268 , SER L:299 , VAL L:300 , SER L:301 , GLN L:336 , MET L:373 , PHE L:374 , HOH L:624 , HOH L:667 , HOH L:761 , HOH L:812 , HOH L:918 , HOH L:953 , HOH L:964
BINDING SITE FOR RESIDUE COY L 601
8
AC8
SOFTWARE
HIS L:143 , GLU L:170 , GLU L:221 , THR L:222 , GLN L:296 , ASP L:335 , GLN L:336 , SER L:362 , K L:603
BINDING SITE FOR RESIDUE PGO L 602
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
All Exons
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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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1egvg_ (G:)
1b: SCOP_d1egvm_ (M:)
2a: SCOP_d1egvb_ (B:)
2b: SCOP_d1egve_ (E:)
3a: SCOP_d1egva_ (A:)
3b: SCOP_d1egvl_ (L:)
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Classes
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)
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(
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Superfamilies
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(
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Open three-helical up-and-down bundle
(49)
Superfamily
:
Diol dehydratase, gamma subunit
(10)
Family
:
Diol dehydratase, gamma subunit
(10)
Protein domain
:
Diol dehydratase, gamma subunit
(10)
Klebsiella oxytoca [TaxId: 571]
(8)
1a
d1egvg_
G:
1b
d1egvm_
M:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
B12-dependent dehydatase associated subunit
(14)
Family
:
Diol dehydratase, beta subunit
(10)
Protein domain
:
Diol dehydratase, beta subunit
(10)
Klebsiella oxytoca [TaxId: 571]
(8)
2a
d1egvb_
B:
2b
d1egve_
E:
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Cobalamin (vitamin B12)-dependent enzymes
(30)
Family
:
Diol dehydratase, alpha subunit
(10)
Protein domain
:
Diol dehydratase, alpha subunit
(9)
Klebsiella oxytoca [TaxId: 571]
(7)
3a
d1egva_
A:
3b
d1egvl_
L:
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1egvB00 (B:46-223)
1b: CATH_1egvE00 (E:46-223)
2a: CATH_1egvA00 (A:1-551)
2b: CATH_1egvL00 (L:1-551)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Diol Dehydratase; Chain B
(11)
Klebsiella oxytoca. Organism_taxid: 571.
(3)
1a
1egvB00
B:46-223
1b
1egvE00
E:46-223
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.350, no name defined]
(9)
Klebsiella oxytoca. Organism_taxid: 571.
(3)
2a
1egvA00
A:1-551
2b
1egvL00
L:1-551
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain M
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
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Asym.Unit (323 KB)
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