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1NJJ
Biol. Unit 1
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)
]
)
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, 4)
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)
View:
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No.
Name
Count
Type
Full Name
1
GET
2
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
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:22 , ASP A:243 , LEU A:339 , PRO A:340 , GLN A:341 , LEU A:382 , GLU A:384 , ASP A:385
BINDING SITE FOR RESIDUE GET A 601
2
AC2
SOFTWARE
ARG B:22 , CYS B:26 , ASP B:243 , PRO B:340 , GLN B:341 , ARG B:342 , GLU B:343 , LEU B:382 , GLU B:384 , ASP B:385 , HOH B:629 , HOH B:631
BINDING SITE FOR RESIDUE GET B 602
3
AC4
SOFTWARE
LYS A:69 , ASP A:88 , HIS A:197 , GLY A:236 , GLY A:237 , GLU A:274 , GLY A:276 , ARG A:277 , TYR A:331 , ASP A:332 , TYR A:389 , HOH A:610 , HOH A:632 , TYR B:323 , CYS B:360 , ASP B:361 , GLY B:362
BINDING SITE FOR RESIDUE ORX A 602
4
AC5
SOFTWARE
TYR A:323 , CYS A:360 , ASP A:361 , LYS B:69 , ASP B:88 , ARG B:154 , HIS B:197 , GLY B:236 , GLY B:237 , GLU B:274 , GLY B:276 , ARG B:277 , TYR B:331 , ASP B:332 , TYR B:389 , HOH B:604
BINDING SITE FOR RESIDUE ORX B 603
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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.
(no "Exon" information available for biological units yet)
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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)
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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
(0, 0)
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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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