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1NJJ
Biol. Unit 2
Info
Asym.Unit (239 KB)
Biol.Unit 1 (118 KB)
Biol.Unit 2 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE DETERMINATION OF T. BRUCEI ORNITHINE DECARBOXYLASE BOUND TO D-ORNITHINE AND TO G418
Authors
:
L. K. Jackson, E. J. Goldsmith, M. A. Phillips
Date
:
31 Dec 02 (Deposition) - 26 Aug 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Ornithine Decarboxylase, Odc, Plp, Pyridoxal 5'-Phosphate, D-Ornithine, G418, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
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Reference
:
L. K. Jackson, E. J. Goldsmith, M. A. Phillips
X-Ray Structure Determination Of Trypanosoma Brucei Ornithine Decarboxylase Bound To D-Ornithine And To G418: Insights Into Substrate Binding And Odc Conformational Flexibility.
J. Biol. Chem. V. 278 22037 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: GENETICIN (GETa)
1b: GENETICIN (GETb)
1c: GENETICIN (GETc)
2a: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (ORXa)
2b: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (ORXb)
2c: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (ORXc)
2d: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (ORXd)
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No.
Name
Count
Type
Full Name
1
GET
1
Ligand/Ion
GENETICIN
2
ORX
2
Ligand/Ion
N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
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Sites
(3, 3)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ARG C:22 , ASP C:243 , PRO C:340 , GLN C:341 , GLU C:343 , LEU C:382 , GLU C:384 , ASP C:385
BINDING SITE FOR RESIDUE GET C 603
2
AC6
SOFTWARE
LYS C:69 , ASP C:88 , ARG C:154 , HIS C:197 , GLY C:236 , GLY C:237 , GLU C:274 , GLY C:276 , ARG C:277 , TYR C:331 , ASP C:332 , TYR C:389 , HOH C:634 , HOH C:652 , TYR D:323 , CYS D:360 , ASP D:361 , HOH D:467
BINDING SITE FOR RESIDUE ORX C 604
3
AC7
SOFTWARE
CYS C:360 , ASP C:361 , GLY C:362 , LYS D:69 , ASP D:88 , HIS D:197 , GLY D:237 , GLU D:274 , PRO D:275 , GLY D:276 , ARG D:277 , TYR D:331 , ASP D:332 , TYR D:389 , HOH D:434 , HOH D:438 , HOH D:442
BINDING SITE FOR RESIDUE ORX D 426
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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
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1njja1 (A:20-43,A:284-414)
1b: SCOP_d1njjb1 (B:20-43,B:284-409)
1c: SCOP_d1njjc1 (C:14-43,C:284-409)
1d: SCOP_d1njjd1 (D:20-43,D:284-409)
2a: SCOP_d1njja2 (A:44-283)
2b: SCOP_d1njjb2 (B:44-283)
2c: SCOP_d1njjc2 (C:44-283)
2d: SCOP_d1njjd2 (D:44-283)
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)
(
)
Protein Domains
(
)
(
)
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
d1njja1
A:20-43,A:284-414
1b
d1njjb1
B:20-43,B:284-409
1c
d1njjc1
C:14-43,C:284-409
1d
d1njjd1
D:20-43,D:284-409
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
d1njja2
A:44-283
2b
d1njjb2
B:44-283
2c
d1njjc2
C:44-283
2d
d1njjd2
D:44-283
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1njjA02 (A:46-279)
1b: CATH_1njjB02 (B:46-279)
1c: CATH_1njjC02 (C:46-279)
1d: CATH_1njjD02 (D:46-279)
2a: CATH_1njjA01 (A:27-45,A:280-409)
2b: CATH_1njjD01 (D:29-45,D:280-405)
2c: CATH_1njjB01 (B:29-45,B:280-405)
2d: CATH_1njjC01 (C:27-45,C:280-404)
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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 gambiense. Organism_taxid: 31285. Strain: gambiense.
(1)
1a
1njjA02
A:46-279
1b
1njjB02
B:46-279
1c
1njjC02
C:46-279
1d
1njjD02
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 gambiense. Organism_taxid: 31285. Strain: gambiense.
(1)
2a
1njjA01
A:27-45,A:280-409
2b
1njjD01
D:29-45,D:280-405
2c
1njjB01
B:29-45,B:280-405
2d
1njjC01
C:27-45,C:280-404
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (239 KB)
Header - Asym.Unit
Biol.Unit 1 (118 KB)
Header - Biol.Unit 1
Biol.Unit 2 (119 KB)
Header - Biol.Unit 2
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