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3N75
Biol. Unit 1
Info
Asym.Unit (656 KB)
Biol.Unit 1, α-C (1.3 MB)
Biol.Unit 1 (1.3 MB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI INDUCIBLE LYSINE DECARBOXYLASE LDCI
Authors
:
U. Kanjee, E. Alexopoulos, E. F. Pai, W. A. Houry
Date
:
26 May 10 (Deposition) - 16 Feb 11 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (2x)
Keywords
:
Pyridoxal-5'-Phosphate Dependent Decarboxylase, Acid Stress Response, Stringent Response, Guanosine Tetraphosphate (Ppgpp), Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Kanjee, I. Gutsche, E. Alexopoulos, B. Zhao, M. El Bakkouri, G. Thibault, K. Liu, S. Ramachandran, J. Snider, E. F. Pai, W. A. Houry
Linkage Between The Bacterial Acid Stress And Stringent Responses: The Structure Of The Inducible Lysine Decarboxylase.
Embo J. V. 30 931 2011
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(4, 40)
Info
All Hetero Components
1a: GUANOSINE-5',3'-TETRAPHOSPHATE (G4Pa)
1b: GUANOSINE-5',3'-TETRAPHOSPHATE (G4Pb)
1c: GUANOSINE-5',3'-TETRAPHOSPHATE (G4Pc)
1d: GUANOSINE-5',3'-TETRAPHOSPHATE (G4Pd)
1e: GUANOSINE-5',3'-TETRAPHOSPHATE (G4Pe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPa)
3b: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPb)
3c: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPc)
3d: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPd)
3e: 2-LYSINE(3-HYDROXY-2-METHYL-5-PHOS... (LLPe)
4a: HEXAETHYLENE GLYCOL (P6Ga)
4b: HEXAETHYLENE GLYCOL (P6Gb)
4c: HEXAETHYLENE GLYCOL (P6Gc)
4d: HEXAETHYLENE GLYCOL (P6Gd)
4e: HEXAETHYLENE GLYCOL (P6Ge)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G4P
10
Ligand/Ion
GUANOSINE-5',3'-TETRAPHOSPHATE
2
GOL
10
Ligand/Ion
GLYCEROL
3
LLP
10
Mod. Amino Acid
2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)
4
P6G
10
Ligand/Ion
HEXAETHYLENE GLYCOL
[
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]
Sites
(15, 15)
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:97 , ARG A:206 , LYS A:417 , GLY A:418 , HOH A:2524 , HOH A:3224 , HOH A:3228 , HOH A:3230 , HOH A:3237 , ARG D:558 , LEU D:564 , ARG D:565 , ASN D:568 , ARG D:585 , HOH D:2335
BINDING SITE FOR RESIDUE G4P A 716
02
AC2
SOFTWARE
HIS A:9 , GLU A:16 , ARG A:20 , TYR A:35 , HOH A:1358 , HOH A:2141
BINDING SITE FOR RESIDUE P6G A 717
03
AC3
SOFTWARE
HIS A:282 , ASP A:323
BINDING SITE FOR RESIDUE GOL A 718
04
AC4
SOFTWARE
ARG B:97 , ARG B:206 , LYS B:417 , GLY B:418 , HOH B:3225 , HOH B:3231 , ARG E:558 , LEU E:564 , ARG E:565 , ASN E:568 , ARG E:585 , HOH E:3235
BINDING SITE FOR RESIDUE G4P B 716
05
AC5
SOFTWARE
HIS B:9 , ARG B:20 , TYR B:35 , HOH B:1872 , HOH B:2157 , HOH B:2958
BINDING SITE FOR RESIDUE P6G B 717
06
AC6
SOFTWARE
HIS B:282 , TRP B:297
BINDING SITE FOR RESIDUE GOL B 718
07
AC7
SOFTWARE
ARG A:558 , LEU A:564 , ARG A:565 , ASN A:568 , ARG A:585 , ARG C:97 , ARG C:206 , LYS C:417 , GLY C:418 , HOH C:1862 , HOH C:2111 , HOH C:2130 , HOH C:2198 , HOH C:3262
BINDING SITE FOR RESIDUE G4P C 716
08
AC8
SOFTWARE
ASN C:8 , HIS C:9 , GLU C:16 , ARG C:20 , TYR C:35 , HOH C:1874 , HOH C:2138 , HOH C:3120
BINDING SITE FOR RESIDUE P6G C 717
09
AC9
SOFTWARE
HIS C:282
BINDING SITE FOR RESIDUE GOL C 718
10
BC1
SOFTWARE
ARG B:558 , LEU B:564 , ARG B:565 , ASN B:568 , ARG B:585 , HOH B:3232 , ARG D:97 , ARG D:206 , LYS D:417 , GLY D:418 , HOH D:1859 , HOH D:2183 , HOH D:3236 , HOH D:3274
BINDING SITE FOR RESIDUE G4P D 716
11
BC2
SOFTWARE
ASN D:8 , HIS D:9 , GLU D:16 , ARG D:20 , HOH D:1879
BINDING SITE FOR RESIDUE P6G D 717
12
BC3
SOFTWARE
HIS D:282 , TRP D:297
BINDING SITE FOR RESIDUE GOL D 718
13
BC4
SOFTWARE
ARG C:558 , LEU C:562 , LEU C:564 , ARG C:565 , ASN C:568 , ARG C:585 , ARG E:97 , ARG E:206 , LYS E:417 , GLY E:418 , HOH E:1832 , HOH E:2573 , HOH E:3223 , HOH E:3227 , HOH E:3229 , HOH E:3233 , HOH E:3234 , HOH E:3265 , HOH E:3269 , HOH E:3271 , HOH E:3272
BINDING SITE FOR RESIDUE G4P E 716
14
BC5
SOFTWARE
HIS E:9 , GLU E:16 , ARG E:20 , TYR E:35 , HOH E:2145
BINDING SITE FOR RESIDUE P6G E 717
15
BC6
SOFTWARE
HIS E:282 , TRP E:297 , ASP E:323
BINDING SITE FOR RESIDUE GOL E 718
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 10)
Info
All PROSITE Patterns/Profiles
1: OKR_DC_1 (A:362-376,B:362-376,C:362-376,D:36...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
OKR_DC_1
PS00703
Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site.
LDCI_ECOLI
362-376
10
A:362-376
B:362-376
C:362-376
D:362-376
E:362-376
[
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Exons
(0, 0)
Info
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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
(0, 0)
Info
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(3, 15)
Info
all PFAM domains
1a: PFAM_OKR_DC_1_N_3n75E01 (E:14-124)
1b: PFAM_OKR_DC_1_N_3n75E02 (E:14-124)
1c: PFAM_OKR_DC_1_N_3n75E03 (E:14-124)
1d: PFAM_OKR_DC_1_N_3n75E04 (E:14-124)
1e: PFAM_OKR_DC_1_N_3n75E05 (E:14-124)
2a: PFAM_OKR_DC_1_3n75E06 (E:130-545)
2b: PFAM_OKR_DC_1_3n75E07 (E:130-545)
2c: PFAM_OKR_DC_1_3n75E08 (E:130-545)
2d: PFAM_OKR_DC_1_3n75E09 (E:130-545)
2e: PFAM_OKR_DC_1_3n75E10 (E:130-545)
3a: PFAM_OKR_DC_1_C_3n75E11 (E:570-704)
3b: PFAM_OKR_DC_1_C_3n75E12 (E:570-704)
3c: PFAM_OKR_DC_1_C_3n75E13 (E:570-704)
3d: PFAM_OKR_DC_1_C_3n75E14 (E:570-704)
3e: PFAM_OKR_DC_1_C_3n75E15 (E:570-704)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CheY
(97)
Family
:
OKR_DC_1_N
(3)
Escherichia coli (strain K12)
(2)
1a
OKR_DC_1_N-3n75E01
E:14-124
1b
OKR_DC_1_N-3n75E02
E:14-124
1c
OKR_DC_1_N-3n75E03
E:14-124
1d
OKR_DC_1_N-3n75E04
E:14-124
1e
OKR_DC_1_N-3n75E05
E:14-124
Clan
:
PLP_aminotran
(240)
Family
:
OKR_DC_1
(3)
Escherichia coli (strain K12)
(2)
2a
OKR_DC_1-3n75E06
E:130-545
2b
OKR_DC_1-3n75E07
E:130-545
2c
OKR_DC_1-3n75E08
E:130-545
2d
OKR_DC_1-3n75E09
E:130-545
2e
OKR_DC_1-3n75E10
E:130-545
Clan
:
no clan defined [family: OKR_DC_1_C]
(3)
Family
:
OKR_DC_1_C
(3)
Escherichia coli (strain K12)
(2)
3a
OKR_DC_1_C-3n75E11
E:570-704
3b
OKR_DC_1_C-3n75E12
E:570-704
3c
OKR_DC_1_C-3n75E13
E:570-704
3d
OKR_DC_1_C-3n75E14
E:570-704
3e
OKR_DC_1_C-3n75E15
E:570-704
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