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1N13
Biol. Unit 1
Info
Asym.Unit (173 KB)
Biol.Unit 1 (87 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE FROM METHANOCOCCUS JANNASHII
Authors
:
W. D. Tolbert, D. E. Graham, R. H. White, S. E. Ealick
Date
:
16 Oct 02 (Deposition) - 25 Mar 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Pyruvoyl Group, Pyruvate, Arginine Decarboxylase, Agmatine, Arginine, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
W. D. Tolbert, D. E. Graham, R. H. White, S. E. Ealick
Pyruvoyl-Dependent Arginine Decarboxylase From Methanococcus Jannaschii: Crystal Structures Of The Self-Cleaved And S53A Proenzyme Forms
Structure V. 11 285 2003
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: AGMATINE (AG2a)
1b: AGMATINE (AG2b)
1c: AGMATINE (AG2c)
1d: AGMATINE (AG2d)
1e: AGMATINE (AG2e)
1f: AGMATINE (AG2f)
2a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
2b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
2c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
2d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
2e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
2f: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDf)
2g: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDg)
2h: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDh)
3a: PYRUVIC ACID (PYRa)
3b: PYRUVIC ACID (PYRb)
3c: PYRUVIC ACID (PYRc)
3d: PYRUVIC ACID (PYRd)
3e: PYRUVIC ACID (PYRe)
3f: PYRUVIC ACID (PYRf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AG2
3
Ligand/Ion
AGMATINE
2
MRD
4
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
3
PYR
3
Mod. Amino Acid
PYRUVIC ACID
[
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]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:52 , HOH A:6663 , PYR B:53 , ILE B:107 , GLU B:109 , LEU C:31 , ASP C:35 , LEU C:38 , GLY C:44 , VAL C:46
BINDING SITE FOR RESIDUE AG2 B 7011
2
AC5
SOFTWARE
SER C:52 , PYR D:53 , ILE D:107 , GLU D:109 , HOH D:6661 , LEU E:31 , ASP E:35 , LEU E:38 , GLY E:44 , VAL E:46
BINDING SITE FOR RESIDUE AG2 D 7015
3
AC6
SOFTWARE
PHE A:34 , ASP A:35 , LEU A:38 , GLY A:44 , VAL A:46 , SER E:52 , PYR F:53 , ILE F:107 , GLU F:109 , HOH F:6655
BINDING SITE FOR RESIDUE AG2 F 7016
4
AC7
SOFTWARE
TYR D:77 , TYR D:79 , HOH D:6656
BINDING SITE FOR RESIDUE MRD D 7001
5
BC2
SOFTWARE
LEU E:31 , PHE E:34 , TYR F:77 , TYR F:79 , ILE F:81 , HOH F:6020 , HOH F:6673
BINDING SITE FOR RESIDUE MRD F 7005
6
BC3
SOFTWARE
LEU A:31 , PHE A:34 , TYR B:77 , TYR B:79 , ILE B:81 , HOH B:6653
BINDING SITE FOR RESIDUE MRD B 7006
7
BC5
SOFTWARE
GLU D:132 , GLY D:135 , TRP D:136 , GLY F:135 , TRP F:136 , HOH F:6290 , HOH F:6320
BINDING SITE FOR RESIDUE MRD D 7008
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1n13_1 (A:,B:)
1b: SCOP_d1n13_2 (C:,D:)
1c: SCOP_d1n13_3 (E:,F:)
1d: SCOP_d1n13_4 (G:,H:)
1e: SCOP_d1n13_5 (I:,J:)
1f: SCOP_d1n13_6 (K:,L:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Pyruvoyl-dependent histidine and arginine decarboxylases
(10)
Superfamily
:
Pyruvoyl-dependent histidine and arginine decarboxylases
(10)
Family
:
Arginine decarboxylase
(4)
Protein domain
:
Arginine decarboxylase
(3)
Methanococcus jannaschii [TaxId: 2190]
(3)
1a
d1n13.1
A:,B:
1b
d1n13.2
C:,D:
1c
d1n13.3
E:,F:
1d
d1n13.4
G:,H:
1e
d1n13.5
I:,J:
1f
d1n13.6
K:,L:
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1n13E00 (E:3-52)
1b: CATH_1n13I00 (I:4-52)
1c: CATH_1n13C00 (C:5-52)
1d: CATH_1n13A00 (A:7-52)
1e: CATH_1n13K00 (K:10-52)
1f: CATH_1n13G00 (G:12-52)
2a: CATH_1n13B00 (B:54-165)
2b: CATH_1n13D00 (D:54-165)
2c: CATH_1n13F00 (F:54-165)
2d: CATH_1n13H00 (H:54-165)
2e: CATH_1n13J00 (J:54-165)
2f: CATH_1n13L00 (L:54-165)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Wheat Germ Agglutinin (Isolectin 2); domain 1
(140)
Homologous Superfamily
:
[code=3.30.60.30, no name defined]
(93)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(4)
1a
1n13E00
E:3-52
1b
1n13I00
I:4-52
1c
1n13C00
C:5-52
1d
1n13A00
A:7-52
1e
1n13K00
K:10-52
1f
1n13G00
G:12-52
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
Pyruvoyl-Dependent Histidine Decarboxylase; Chain B
(11)
Homologous Superfamily
:
Pyruvoyl-Dependent Histidine Decarboxylase, subunit B
(11)
Methanocaldococcus jannaschii. Organism_taxid: 2190.
(5)
2a
1n13B00
B:54-165
2b
1n13D00
D:54-165
2c
1n13F00
F:54-165
2d
1n13H00
H:54-165
2e
1n13J00
J:54-165
2f
1n13L00
L:54-165
[
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Pfam Domains
(1, 12)
Info
all PFAM domains
1a: PFAM_PvlArgDC_1n13L01 (L:54-164)
1b: PFAM_PvlArgDC_1n13L02 (L:54-164)
1c: PFAM_PvlArgDC_1n13L03 (L:54-164)
1d: PFAM_PvlArgDC_1n13L04 (L:54-164)
1e: PFAM_PvlArgDC_1n13L05 (L:54-164)
1f: PFAM_PvlArgDC_1n13L06 (L:54-164)
1g: PFAM_PvlArgDC_1n13L07 (L:54-164)
1h: PFAM_PvlArgDC_1n13L08 (L:54-164)
1i: PFAM_PvlArgDC_1n13L09 (L:54-164)
1j: PFAM_PvlArgDC_1n13L10 (L:54-164)
1k: PFAM_PvlArgDC_1n13L11 (L:54-164)
1l: PFAM_PvlArgDC_1n13L12 (L:54-164)
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)
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)
(
)
Clan
:
no clan defined [family: PvlArgDC]
(4)
Family
:
PvlArgDC
(4)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth
(4)
1a
PvlArgDC-1n13L01
L:54-164
1b
PvlArgDC-1n13L02
L:54-164
1c
PvlArgDC-1n13L03
L:54-164
1d
PvlArgDC-1n13L04
L:54-164
1e
PvlArgDC-1n13L05
L:54-164
1f
PvlArgDC-1n13L06
L:54-164
1g
PvlArgDC-1n13L07
L:54-164
1h
PvlArgDC-1n13L08
L:54-164
1i
PvlArgDC-1n13L09
L:54-164
1j
PvlArgDC-1n13L10
L:54-164
1k
PvlArgDC-1n13L11
L:54-164
1l
PvlArgDC-1n13L12
L:54-164
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