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2TOD
Asym. Unit
Info
Asym.Unit (250 KB)
Biol.Unit 1 (123 KB)
Biol.Unit 2 (124 KB)
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(1)
Title
:
ORNITHINE DECARBOXYLASE FROM TRYPANOSOMA BRUCEI K69A MUTANT IN COMPLEX WITH ALPHA-DIFLUOROMETHYLORNITHINE
Authors
:
N. V. Grishin, A. L. Osterman, H. B. Brooks, M. A. Phillips, E. J. Goldsmi
Date
:
18 May 99 (Deposition) - 17 Nov 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Polyamine Metabolism, Pyridoxal 5'-Phosphate, Alpha-Beta Barrel, Lyase
(Keyword Search:
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Reference
:
N. V. Grishin, A. L. Osterman, H. B. Brooks, M. A. Phillips, E. J. Goldsmith
X-Ray Structure Of Ornithine Decarboxylase From Trypanosoma Brucei: The Native Structure And The Structure In Complex With Alpha-Difluoromethylornithine.
Biochemistry V. 38 15174 1999
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: ALPHA-DIFLUOROMETHYLORNITHINE (DMOa)
1b: ALPHA-DIFLUOROMETHYLORNITHINE (DMOb)
1c: ALPHA-DIFLUOROMETHYLORNITHINE (DMOc)
1d: ALPHA-DIFLUOROMETHYLORNITHINE (DMOd)
2a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
2b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
2c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
2d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMO
4
Ligand/Ion
ALPHA-DIFLUOROMETHYLORNITHINE
2
PLP
4
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(12, 12)
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: CAA (AUTHOR)
10: CAB (AUTHOR)
11: CAC (AUTHOR)
12: CAD (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:360 , DMO A:700 , ALA B:67 , ARG B:154 , HIS B:197 , SER B:200 , GLY B:236 , GLY B:237 , GLU B:274 , GLY B:276 , ARG B:277 , TYR B:389 , HOH B:708 , HOH B:741
BINDING SITE FOR RESIDUE PLP B 600
02
AC2
SOFTWARE
CYS A:360 , ASP A:361 , PHE A:397 , HOH A:728 , TYR B:331 , ASP B:332 , PLP B:600
BINDING SITE FOR RESIDUE DMO A 700
03
AC3
SOFTWARE
ASP A:88 , ARG A:154 , HIS A:197 , SER A:200 , GLY A:236 , GLY A:237 , GLU A:274 , GLY A:276 , ARG A:277 , TYR A:389 , HOH A:719 , HOH A:768 , CYS B:360 , DMO B:700
BINDING SITE FOR RESIDUE PLP A 600
04
AC4
SOFTWARE
TYR A:331 , ASP A:332 , PLP A:600 , CYS B:360 , ASP B:361 , PHE B:397 , HOH B:707 , HOH B:757
BINDING SITE FOR RESIDUE DMO B 700
05
AC5
SOFTWARE
CYS C:360 , DMO C:700 , ALA D:67 , ARG D:154 , HIS D:197 , SER D:200 , GLY D:236 , GLY D:237 , GLU D:274 , PRO D:275 , GLY D:276 , ARG D:277 , TYR D:389 , HOH D:715 , HOH D:730
BINDING SITE FOR RESIDUE PLP D 600
06
AC6
SOFTWARE
CYS C:360 , ASP C:361 , PHE C:397 , HOH C:714 , HOH C:773 , TYR D:331 , ASP D:332 , PLP D:600
BINDING SITE FOR RESIDUE DMO C 700
07
AC7
SOFTWARE
ALA C:67 , ASP C:88 , ARG C:154 , HIS C:197 , SER C:200 , GLY C:236 , GLY C:237 , GLU C:274 , GLY C:276 , ARG C:277 , TYR C:389 , HOH C:711 , HOH C:752 , HOH C:813 , CYS D:360 , DMO D:700
BINDING SITE FOR RESIDUE PLP C 600
08
AC8
SOFTWARE
TYR C:331 , ASP C:332 , PLP C:600 , CYS D:360 , ASP D:361 , PHE D:397 , HOH D:708 , HOH D:725
BINDING SITE FOR RESIDUE DMO D 700
09
CAA
AUTHOR
ALA A:69 , ARG A:154 , GLU A:274 , HIS A:197 , GLY A:237 , SER A:200 , ARG A:277 , CYS A:360 , TYR A:389 , ASP A:332 , TYR A:331 , TYR A:323 , PHE A:397 , ASP A:361
CATALYTIC SITE
10
CAB
AUTHOR
ALA B:69 , ARG B:154 , GLU B:274 , HIS B:197 , GLY B:237 , SER B:200 , ARG B:277 , CYS B:360 , TYR B:389 , ASP B:332 , TYR B:331 , TYR B:323 , PHE B:397 , ASP B:361
CATALYTIC SITE
11
CAC
AUTHOR
ALA C:69 , ARG C:154 , GLU C:274 , HIS C:197 , GLY C:237 , SER C:200 , ARG C:277 , CYS C:360 , TYR C:389 , ASP C:332 , TYR C:331 , TYR C:323 , PHE C:397 , ASP C:361
CATALYTIC SITE
12
CAD
AUTHOR
ALA D:69 , ARG D:154 , GLU D:274 , HIS D:197 , GLY D:237 , SER D:200 , ARG D:277 , CYS D:360 , TYR D:389 , ASP D:332 , TYR D:331 , TYR D:323 , PHE D:397 , ASP D:361
CATALYTIC SITE
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ODR_DC_2_1 (A:66-84,B:66-84,C:66-84,D:66-84)
2: ODR_DC_2_2 (A:222-239,B:222-239,C:222-239,D:22...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ODR_DC_2_1
PS00878
Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
DCOR_TRYBB
64-82
4
A:66-84
B:66-84
C:66-84
D:66-84
2
ODR_DC_2_2
PS00879
Orn/DAP/Arg decarboxylases family 2 signature 2.
DCOR_TRYBB
220-237
4
A:222-239
B:222-239
C:222-239
D:222-239
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2toda1 (A:37-43,A:284-410)
1b: SCOP_d2todb1 (B:37-43,B:284-410)
1c: SCOP_d2todc1 (C:37-43,C:284-410)
1d: SCOP_d2todd1 (D:37-43,D:284-410)
2a: SCOP_d2toda2 (A:44-283)
2b: SCOP_d2todb2 (B:44-283)
2c: SCOP_d2todc2 (C:44-283)
2d: SCOP_d2todd2 (D:44-283)
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Class
:
All beta proteins
(24004)
Fold
:
Domain of alpha and beta subunits of F1 ATP synthase-like
(89)
Superfamily
:
Alanine racemase C-terminal domain-like
(25)
Family
:
Eukaryotic ODC-like
(13)
Protein domain
:
Eukaryotic ornithine decarboxylase (ODC)
(7)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(5)
1a
d2toda1
A:37-43,A:284-410
1b
d2todb1
B:37-43,B:284-410
1c
d2todc1
C:37-43,C:284-410
1d
d2todd1
D:37-43,D:284-410
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
PLP-binding barrel
(27)
Family
:
Alanine racemase-like, N-terminal domain
(25)
Protein domain
:
Eukaryotic ornithine decarboxylase
(7)
Trypanosome (Trypanosoma brucei) [TaxId: 5691]
(5)
2a
d2toda2
A:44-283
2b
d2todb2
B:44-283
2c
d2todc2
C:44-283
2d
d2todd2
D:44-283
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2todA02 (A:46-279)
1b: CATH_2todC02 (C:46-279)
1c: CATH_2todD02 (D:46-279)
1d: CATH_2todB02 (B:46-279)
2a: CATH_2todA01 (A:37-45,A:280-408)
2b: CATH_2todC01 (C:37-45,C:280-408)
2c: CATH_2todD01 (D:37-45,D:280-408)
2d: CATH_2todB01 (B:37-45,B:280-408)
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Organisms
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)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Alanine racemase
(53)
Trypanosoma brucei. Organism_taxid: 5691.
(3)
1a
2todA02
A:46-279
1b
2todC02
C:46-279
1c
2todD02
D:46-279
1d
2todB02
B:46-279
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Homologous Superfamily
:
Lyase, Ornithine Decarboxylase; Chain A, domain 1
(47)
Trypanosoma brucei. Organism_taxid: 5691.
(3)
2a
2todA01
A:37-45,A:280-408
2b
2todC01
C:37-45,C:280-408
2c
2todD01
D:37-45,D:280-408
2d
2todB01
B:37-45,B:280-408
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Orn_Arg_deC_N_2todD01 (D:44-282)
1b: PFAM_Orn_Arg_deC_N_2todD02 (D:44-282)
1c: PFAM_Orn_Arg_deC_N_2todD03 (D:44-282)
1d: PFAM_Orn_Arg_deC_N_2todD04 (D:44-282)
2a: PFAM_Orn_DAP_Arg_deC_2todD05 (D:285-408)
2b: PFAM_Orn_DAP_Arg_deC_2todD06 (D:285-408)
2c: PFAM_Orn_DAP_Arg_deC_2todD07 (D:285-408)
2d: PFAM_Orn_DAP_Arg_deC_2todD08 (D:285-408)
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Clans
(
)
(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Orn_Arg_deC_N
(17)
Trypanosoma brucei brucei
(3)
1a
Orn_Arg_deC_N-2todD01
D:44-282
1b
Orn_Arg_deC_N-2todD02
D:44-282
1c
Orn_Arg_deC_N-2todD03
D:44-282
1d
Orn_Arg_deC_N-2todD04
D:44-282
Clan
:
no clan defined [family: Orn_DAP_Arg_deC]
(18)
Family
:
Orn_DAP_Arg_deC
(18)
Trypanosoma brucei brucei
(3)
2a
Orn_DAP_Arg_deC-2todD05
D:285-408
2b
Orn_DAP_Arg_deC-2todD06
D:285-408
2c
Orn_DAP_Arg_deC-2todD07
D:285-408
2d
Orn_DAP_Arg_deC-2todD08
D:285-408
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