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1QU4
Biol. Unit 1
Info
Asym.Unit (232 KB)
Biol.Unit 1 (115 KB)
Biol.Unit 2 (115 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE DECARBOXYLASE
Authors
:
N. V. Grishin, A. L. Osterman, H. B. Brooks, M. A. Phillips, E. J. Goldsmi
Date
:
06 Jul 99 (Deposition) - 17 Nov 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
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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Gene Ontology, PubMed, Web (Google)
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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
(1, 2)
Info
All Hetero Components
1a: PYRIDOXAL-5'-PHOSPHATE (PLPa)
1b: PYRIDOXAL-5'-PHOSPHATE (PLPb)
1c: PYRIDOXAL-5'-PHOSPHATE (PLPc)
1d: PYRIDOXAL-5'-PHOSPHATE (PLPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PLP
2
Ligand/Ion
PYRIDOXAL-5'-PHOSPHATE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:67 , LYS A:69 , 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 , CYS B:360
BINDING SITE FOR RESIDUE PLP A 600
2
AC2
SOFTWARE
CYS A:360 , ALA B:67 , LYS B:69 , ASP B:88 , 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
BINDING SITE FOR RESIDUE PLP B 600
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ODR_DC_2_1 (A:66-84,B:66-84)
2: ODR_DC_2_2 (A:222-239,B:222-239)
;
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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
2
A:66-84
B:66-84
-
-
2
ODR_DC_2_2
PS00879
Orn/DAP/Arg decarboxylases family 2 signature 2.
DCOR_TRYBB
220-237
2
A:222-239
B:222-239
-
-
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Exons
(0, 0)
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1qu4a1 (A:35-43,A:284-411)
1b: SCOP_d1qu4b1 (B:35-43,B:284-411)
1c: SCOP_d1qu4c1 (C:35-43,C:284-411)
1d: SCOP_d1qu4d1 (D:35-43,D:284-411)
2a: SCOP_d1qu4a2 (A:44-283)
2b: SCOP_d1qu4b2 (B:44-283)
2c: SCOP_d1qu4c2 (C:44-283)
2d: SCOP_d1qu4d2 (D:44-283)
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)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
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
d1qu4a1
A:35-43,A:284-411
1b
d1qu4b1
B:35-43,B:284-411
1c
d1qu4c1
C:35-43,C:284-411
1d
d1qu4d1
D:35-43,D:284-411
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
d1qu4a2
A:44-283
2b
d1qu4b2
B:44-283
2c
d1qu4c2
C:44-283
2d
d1qu4d2
D:44-283
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1qu4A02 (A:46-279)
1b: CATH_1qu4B02 (B:46-279)
1c: CATH_1qu4C02 (C:46-279)
1d: CATH_1qu4D02 (D:46-279)
2a: CATH_1qu4B01 (B:35-45,B:280-409)
2b: CATH_1qu4A01 (A:35-45,A:280-411)
2c: CATH_1qu4C01 (C:35-45,C:280-409)
2d: CATH_1qu4D01 (D:35-45,D:280-409)
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
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
1qu4A02
A:46-279
1b
1qu4B02
B:46-279
1c
1qu4C02
C:46-279
1d
1qu4D02
D: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
1qu4B01
B:35-45,B:280-409
2b
1qu4A01
A:35-45,A:280-411
2c
1qu4C01
C:35-45,C:280-409
2d
1qu4D01
D:35-45,D:280-409
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Orn_Arg_deC_N_1qu4D01 (D:44-282)
1b: PFAM_Orn_Arg_deC_N_1qu4D02 (D:44-282)
1c: PFAM_Orn_Arg_deC_N_1qu4D03 (D:44-282)
1d: PFAM_Orn_Arg_deC_N_1qu4D04 (D:44-282)
2a: PFAM_Orn_DAP_Arg_deC_1qu4D05 (D:285-408)
2b: PFAM_Orn_DAP_Arg_deC_1qu4D06 (D:285-408)
2c: PFAM_Orn_DAP_Arg_deC_1qu4D07 (D:285-408)
2d: PFAM_Orn_DAP_Arg_deC_1qu4D08 (D:285-408)
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Clans
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(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
Orn_Arg_deC_N
(17)
Trypanosoma brucei brucei
(3)
1a
Orn_Arg_deC_N-1qu4D01
D:44-282
1b
Orn_Arg_deC_N-1qu4D02
D:44-282
1c
Orn_Arg_deC_N-1qu4D03
D:44-282
1d
Orn_Arg_deC_N-1qu4D04
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-1qu4D05
D:285-408
2b
Orn_DAP_Arg_deC-1qu4D06
D:285-408
2c
Orn_DAP_Arg_deC-1qu4D07
D:285-408
2d
Orn_DAP_Arg_deC-1qu4D08
D:285-408
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