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1RKW
Biol. Unit 2
Info
Asym.Unit (138 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE MULTIDRUG BINDING TRANSCRIPTIONAL REPRESSOR QACR BOUND TO PENTAMADINE
Authors
:
D. S. Murray, M. A. Schumacher, R. G. Brennan
Date
:
23 Nov 03 (Deposition) - 01 Jun 04 (Release) - 30 Jun 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.62
Chains
:
Asym. Unit : A,B,D,E
Biol. Unit 1: A,B (1x)
Biol. Unit 2: D,E (1x)
Keywords
:
Multidrug Recognition, Pent, Qacr, Multidrug Binding Protein, Transcription
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. S. Murray, M. A. Schumacher, R. G. Brennan
Crystal Structures Of Qacr-Diamidine Complexes Reveal Additional Multidrug-Binding Modes And A Novel Mechanism Of Drug Charge Neutralization.
J. Biol. Chem. V. 279 14365 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 14)
Info
All Hetero Components
1a: 1,5-BIS(4-AMIDINOPHENOXY)PENTANE (PNTa)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PNT
-1
Ligand/Ion
1,5-BIS(4-AMIDINOPHENOXY)PENTANE
2
SO4
14
Ligand/Ion
SULFATE ION
[
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Sites
(16, 16)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC2 (SOFTWARE)
15: CC3 (SOFTWARE)
16: CC4 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
THR D:25 , TYR D:40 , THR D:45 , LYS D:46 , SO4 D:799
BINDING SITE FOR RESIDUE SO4 D 499
02
AC6
SOFTWARE
THR E:24 , THR E:25 , GLY E:26 , GLU E:27 , LYS E:36
BINDING SITE FOR RESIDUE SO4 E 599
03
AC7
SOFTWARE
LYS B:66 , ASN D:2 , LEU D:3 , LYS D:4 , ASN D:38 , HIS D:42
BINDING SITE FOR RESIDUE SO4 D 219
04
AC8
SOFTWARE
THR D:24 , GLY D:26
BINDING SITE FOR RESIDUE SO4 D 229
05
AC9
SOFTWARE
LYS E:36 , TYR E:40 , THR E:45 , LYS E:46
BINDING SITE FOR RESIDUE SO4 E 239
06
BC1
SOFTWARE
VAL A:29 , SER A:35 , LYS A:36 , LYS E:60
BINDING SITE FOR RESIDUE SO4 A 699
07
BC2
SOFTWARE
TYR D:20 , LYS D:46 , GLU D:105 , TYR D:106 , SO4 D:499
BINDING SITE FOR RESIDUE SO4 D 799
08
BC3
SOFTWARE
LYS E:12 , ILE E:53 , ILE E:56 , GLU E:57
BINDING SITE FOR RESIDUE SO4 E 899
09
BC4
SOFTWARE
LYS A:36 , TYR A:40 , ASN E:2 , ASP E:5 , LYS E:6
BINDING SITE FOR RESIDUE SO4 E 999
10
BC5
SOFTWARE
LYS E:4 , HIS E:42
BINDING SITE FOR RESIDUE SO4 E 249
11
BC6
SOFTWARE
GLN B:64 , TYR B:91 , GLN D:64 , TYR D:91
BINDING SITE FOR RESIDUE SO4 B 259
12
BC9
SOFTWARE
ILE B:70 , LYS B:73 , HIS D:164 , GLN D:166 , TYR E:107
BINDING SITE FOR RESIDUE SO4 D 289
13
CC1
SOFTWARE
HIS E:128 , LYS E:132
BINDING SITE FOR RESIDUE SO4 E 209
14
CC2
SOFTWARE
LYS D:17 , LYS D:30 , GLU D:33
BINDING SITE FOR RESIDUE SO4 D 779
15
CC3
SOFTWARE
ASN A:2 , TYR D:107
BINDING SITE FOR RESIDUE SO4 D 539
16
CC4
SOFTWARE
LYS D:173 , ASN E:143 , ASP E:144 , ALA E:147
BINDING SITE FOR RESIDUE SO4 D 639
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: HTH_TETR_1 (D:19-49,E:19-49)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_TETR_1
PS01081
TetR-type HTH domain signature.
QACR_STAAU
19-49
2
-
-
D:19-49
E:19-49
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1rkwa1 (A:2-72)
1b: SCOP_d1rkwb1 (B:2-72)
1c: SCOP_d1rkwd1 (D:2-72)
1d: SCOP_d1rkwe1 (E:2-72)
2a: SCOP_d1rkwa2 (A:73-187)
2b: SCOP_d1rkwb2 (B:73-187)
2c: SCOP_d1rkwd2 (D:73-187)
2d: SCOP_d1rkwe2 (E:73-187)
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Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Homeodomain-like
(373)
Family
:
Tetracyclin repressor-like, N-terminal domain
(97)
Protein domain
:
Multidrug binding protein QacR
(24)
Staphylococcus aureus [TaxId: 1280]
(24)
1a
d1rkwa1
A:2-72
1b
d1rkwb1
B:2-72
1c
d1rkwd1
D:2-72
1d
d1rkwe1
E:2-72
Fold
:
Tetracyclin repressor-like, C-terminal domain
(116)
Superfamily
:
Tetracyclin repressor-like, C-terminal domain
(116)
Family
:
Tetracyclin repressor-like, C-terminal domain
(114)
Protein domain
:
Multidrug binding protein QacR
(24)
Staphylococcus aureus [TaxId: 1280]
(24)
2a
d1rkwa2
A:73-187
2b
d1rkwb2
B:73-187
2c
d1rkwd2
D:73-187
2d
d1rkwe2
E:73-187
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1rkwA01 (A:2-50)
1b: CATH_1rkwB01 (B:2-50)
1c: CATH_1rkwD01 (D:2-50)
1d: CATH_1rkwE01 (E:2-50)
2a: CATH_1rkwA02 (A:51-187)
2b: CATH_1rkwB02 (B:51-187)
2c: CATH_1rkwD02 (D:51-187)
2d: CATH_1rkwE02 (E:51-187)
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(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Homeodomain-like
(288)
Staphylococcus aureus. Organism_taxid: 1280.
(8)
1a
1rkwA01
A:2-50
1b
1rkwB01
B:2-50
1c
1rkwD01
D:2-50
1d
1rkwE01
E:2-50
Topology
:
Tetracycline Repressor; domain 2
(126)
Homologous Superfamily
:
Tetracycline Repressor, domain 2
(124)
Staphylococcus aureus. Organism_taxid: 1280.
(7)
2a
1rkwA02
A:51-187
2b
1rkwB02
B:51-187
2c
1rkwD02
D:51-187
2d
1rkwE02
E:51-187
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_TetR_N_1rkwE01 (E:7-53)
1b: PFAM_TetR_N_1rkwE02 (E:7-53)
1c: PFAM_TetR_N_1rkwE03 (E:7-53)
1d: PFAM_TetR_N_1rkwE04 (E:7-53)
2a: PFAM_TetR_C_5_1rkwE05 (E:57-187)
2b: PFAM_TetR_C_5_1rkwE06 (E:57-187)
2c: PFAM_TetR_C_5_1rkwE07 (E:57-187)
2d: PFAM_TetR_C_5_1rkwE08 (E:57-187)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
HTH
(544)
Family
:
TetR_N
(84)
Staphylococcus aureus
(11)
1a
TetR_N-1rkwE01
E:7-53
1b
TetR_N-1rkwE02
E:7-53
1c
TetR_N-1rkwE03
E:7-53
1d
TetR_N-1rkwE04
E:7-53
Clan
:
TetR_C
(33)
Family
:
TetR_C_5
(11)
Staphylococcus aureus
(11)
2a
TetR_C_5-1rkwE05
E:57-187
2b
TetR_C_5-1rkwE06
E:57-187
2c
TetR_C_5-1rkwE07
E:57-187
2d
TetR_C_5-1rkwE08
E:57-187
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