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1XBP
Asym. Unit
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Asym.Unit (1.1 MB)
Biol.Unit 1, α-C (1.1 MB)
Biol.Unit 1 (1.1 MB)
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(1)
Title
:
INHIBITION OF PEPTIDE BOND FORMATION BY PLEUROMUTILINS: THE STRUCTURE OF THE 50S RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS IN COMPLEX WITH TIAMULIN
Authors
:
F. Schluenzen, E. Pyetan, P. Fucini, A. Yonath, J. M. Harms
Date
:
31 Aug 04 (Deposition) - 01 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,W,X,Y,Z,0,1,2,3,4,9
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,W,X,Y,Z,0,1,2,3,4,9 (1x)
Keywords
:
Tiamulin, Pleuromutilin, 50S Ribosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Schluenzen, E. Pyetan, P. Fucini, A. Yonath, J. M. Harms
Inhibition Of Peptide Bond Formation By Pleuromutilins: The Structure Of The 50S Ribosomal Subunit From Deinococcus Radiodurans In Complex With Tiamulin.
Mol. Microbiol. V. 54 1287 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: TIAMULIN (MULa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MUL
1
Ligand/Ion
TIAMULIN
[
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]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
G 0:2044 , C 0:2046 , A 0:2430 , A 0:2482 , U 0:2483 , G 0:2484 , U 0:2485
BINDING SITE FOR RESIDUE MUL 0 2881
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(22, 22)
Info
All PROSITE Patterns/Profiles
01: RIBOSOMAL_L34 (2:2-21)
02: RIBOSOMAL_L35 (3:5-31)
03: RIBOSOMAL_L36 (4:11-36)
04: RIBOSOMAL_L9 (F:12-39)
05: RIBOSOMAL_L24 (S:19-36)
06: RIBOSOMAL_L33 (1:22-41)
07: RIBOSOMAL_L27 (U:34-48)
08: RIBOSOMAL_L31 (Y:34-55)
09: RIBOSOMAL_L17 (L:34-56)
10: RIBOSOMAL_L29 (W:39-53)
11: RIBOSOMAL_L20 (O:54-70)
12: RIBOSOMAL_L16_1 (K:60-71)
13: RIBOSOMAL_L14 (I:72-98)
14: RIBOSOMAL_L23 (R:76-91)
15: RIBOSOMAL_L16_2 (K:83-94)
16: RIBOSOMAL_L19 (N:93-108)
17: RIBOSOMAL_L3 (B:96-119)
18: RIBOSOMAL_L22 (Q:104-128)
19: RIBOSOMAL_L15 (J:107-137)
20: RIBOSOMAL_L11 (G:125-140)
21: RIBOSOMAL_L13 (H:131-153)
22: RIBOSOMAL_L2 (A:219-230)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIBOSOMAL_L34
PS00784
Ribosomal protein L34 signature.
RL34_DEIRA
2-21
1
2:2-21
2
RIBOSOMAL_L35
PS00936
Ribosomal protein L35 signature.
RL35_DEIRA
5-31
1
3:5-31
3
RIBOSOMAL_L36
PS00828
Ribosomal protein L36 signature.
RL36_DEIRA
11-36
1
4:11-36
4
RIBOSOMAL_L9
PS00651
Ribosomal protein L9 signature.
RL9_DEIRA
12-39
1
F:12-39
5
RIBOSOMAL_L24
PS01108
Ribosomal protein L24 signature.
RL24_DEIRA
19-36
1
S:19-36
6
RIBOSOMAL_L33
PS00582
Ribosomal protein L33 signature.
RL33_DEIRA
22-41
1
1:22-41
7
RIBOSOMAL_L27
PS00831
Ribosomal protein L27 signature.
RL27_DEIRA
34-48
1
U:34-48
8
RIBOSOMAL_L31
PS01143
Ribosomal protein L31 signature.
RL31_DEIRA
34-55
1
Y:34-55
9
RIBOSOMAL_L17
PS01167
Ribosomal protein L17 signature.
RL17_DEIRA
34-56
1
L:34-56
10
RIBOSOMAL_L29
PS00579
Ribosomal protein L29 signature.
RL29_DEIRA
39-53
1
W:39-53
11
RIBOSOMAL_L20
PS00937
Ribosomal protein L20 signature.
RL20_DEIRA
54-70
1
O:54-70
12
RIBOSOMAL_L16_1
PS00586
Ribosomal protein L16 signature 1.
RL16_DEIRA
59-70
1
K:60-71
13
RIBOSOMAL_L14
PS00049
Ribosomal protein L14 signature.
RL14_DEIRA
72-98
1
I:72-98
14
RIBOSOMAL_L23
PS00050
Ribosomal protein L23 signature.
RL23_DEIRA
76-91
1
R:76-91
15
RIBOSOMAL_L16_2
PS00701
Ribosomal protein L16 signature 2.
RL16_DEIRA
82-93
1
K:83-94
16
RIBOSOMAL_L19
PS01015
Ribosomal protein L19 signature.
RL19_DEIRA
93-108
1
N:93-108
17
RIBOSOMAL_L3
PS00474
Ribosomal protein L3 signature.
RL3_DEIRA
96-119
1
B:96-119
18
RIBOSOMAL_L22
PS00464
Ribosomal protein L22 signature.
RL22_DEIRA
104-128
1
Q:104-128
19
RIBOSOMAL_L15
PS00475
Ribosomal protein L15 signature.
RL15_DEIRA
107-137
1
J:107-137
20
RIBOSOMAL_L11
PS00359
Ribosomal protein L11 signature.
RL11_DEIRA
125-140
1
G:125-140
21
RIBOSOMAL_L13
PS00783
Ribosomal protein L13 signature.
RL13_DEIRA
131-153
1
H:131-153
22
RIBOSOMAL_L2
PS00467
Ribosomal protein L2 signature.
RL2_DEIRA
219-230
1
A:219-230
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(28, 29)
Info
All SCOP Domains
01a: SCOP_d1xbpg1 (G:72-143)
02a: SCOP_d1xbpw1 (W:2-66)
03a: SCOP_d1xbpo1 (O:2-118)
04a: SCOP_d1xbpu1 (U:2-85)
05a: SCOP_d1xbpp1 (P:5-98)
06a: SCOP_d1xbpa2 (A:33-127)
07a: SCOP_d1xbpb1 (B:1-205)
08a: SCOP_d1xbpi1 (I:2-133)
09a: SCOP_d1xbpt1 (T:1-175)
10a: SCOP_d1xbpa1 (A:128-272)
11a: SCOP_d1xbpn1 (N:2-109)
12a: SCOP_d1xbps1 (S:4-113)
13a: SCOP_d1xbp31 (3:2-64)
14a: SCOP_d1xbpl1 (L:3-115)
15a: SCOP_d1xbpg2 (G:1-71)
16a: SCOP_d1xbpq1 (Q:8-134)
17a: SCOP_d1xbpx1 (X:1-55)
18a: SCOP_d1xbpe1 (E:83-172)
18b: SCOP_d1xbpe2 (E:5-82)
19a: SCOP_d1xbpr1 (R:2-94)
20a: SCOP_d1xbpd1 (D:3-179)
21a: SCOP_d1xbpm1 (M:8-111)
22a: SCOP_d1xbph1 (H:30-171)
23a: SCOP_d1xbpc1 (C:2-198)
24a: SCOP_d1xbpj1 (J:4-144)
25a: SCOP_d1xbp21 (2:1-46)
26a: SCOP_d1xbp41 (4:2-36)
27a: SCOP_d1xbpz1 (Z:2-59)
28a: SCOP_d1xbp11 (1:2-54)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Ribosomal protein L11, C-terminal domain
(96)
Family
:
Ribosomal protein L11, C-terminal domain
(96)
Protein domain
:
Ribosomal protein L11, C-terminal domain
(96)
Deinococcus radiodurans [TaxId: 1299]
(4)
01a
d1xbpg1
G:72-143
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
Ribosomal protein L29 (L29p)
(89)
Family
:
Ribosomal protein L29 (L29p)
(89)
Protein domain
:
Ribosomal protein L29 (L29p)
(89)
Deinococcus radiodurans [TaxId: 1299]
(8)
02a
d1xbpw1
W:2-66
Fold
:
PABP domain-like
(63)
Superfamily
:
Ribosomal protein L20
(51)
Family
:
Ribosomal protein L20
(51)
Protein domain
:
Ribosomal protein L20
(51)
Deinococcus radiodurans [TaxId: 1299]
(6)
03a
d1xbpo1
O:2-118
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Ribosomal L27 protein-like
(52)
Family
:
Ribosomal L27 protein
(42)
Protein domain
:
Ribosomal protein L27
(42)
Deinococcus radiodurans [TaxId: 1299]
(7)
04a
d1xbpu1
U:2-85
Fold
:
L21p-like
(48)
Superfamily
:
L21p-like
(48)
Family
:
Ribosomal protein L21p
(48)
Protein domain
:
Ribosomal protein L21p
(48)
Deinococcus radiodurans [TaxId: 1299]
(6)
05a
d1xbpp1
P:5-98
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Cold shock DNA-binding domain-like
(310)
Protein domain
:
N-terminal domain of ribosomal protein L2
(79)
Deinococcus radiodurans [TaxId: 1299]
(5)
06a
d1xbpa2
A:33-127
Fold
:
Reductase/isomerase/elongation factor common domain
(381)
Superfamily
:
Translation proteins
(218)
Family
:
Ribosomal protein L3
(107)
Protein domain
:
Ribosomal protein L3
(107)
Deinococcus radiodurans [TaxId: 1299]
(9)
07a
d1xbpb1
B:1-205
Fold
:
Ribosomal protein L14
(91)
Superfamily
:
Ribosomal protein L14
(91)
Family
:
Ribosomal protein L14
(91)
Protein domain
:
Ribosomal protein L14
(91)
Deinococcus radiodurans [TaxId: 1299]
(6)
08a
d1xbpi1
I:2-133
Fold
:
Ribosomal protein L25-like
(72)
Superfamily
:
Ribosomal protein L25-like
(72)
Family
:
Ribosomal protein L25-like
(54)
Protein domain
:
Ribosomal protein TL5 (general stress protein CTC)
(22)
Deinococcus radiodurans [TaxId: 1299]
(6)
09a
d1xbpt1
T:1-175
Fold
:
SH3-like barrel
(1035)
Superfamily
:
Translation proteins SH3-like domain
(251)
Family
:
C-terminal domain of ribosomal protein L2
(79)
Protein domain
:
C-terminal domain of ribosomal protein L2
(79)
Deinococcus radiodurans [TaxId: 1299]
(5)
10a
d1xbpa1
A:128-272
Family
:
Ribosomal protein L19
(19)
Protein domain
:
Ribosomal protein L19
(19)
Deinococcus radiodurans [TaxId: 1299]
(6)
11a
d1xbpn1
N:2-109
Family
:
Ribosomal proteins L24p and L21e
(132)
Protein domain
:
Ribosomal proteins L24 (L24p)
(92)
Deinococcus radiodurans [TaxId: 1299]
(7)
12a
d1xbps1
S:4-113
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
L35p-like
(42)
Superfamily
:
L35p-like
(42)
Family
:
Ribosomal protein L35p
(42)
Protein domain
:
Ribosomal protein L35p
(42)
Deinococcus radiodurans [TaxId: 1299]
(6)
13a
d1xbp31
3:2-64
Fold
:
Prokaryotic ribosomal protein L17
(45)
Superfamily
:
Prokaryotic ribosomal protein L17
(45)
Family
:
Prokaryotic ribosomal protein L17
(45)
Protein domain
:
Prokaryotic ribosomal protein L17
(45)
Deinococcus radiodurans [TaxId: 1299]
(6)
14a
d1xbpl1
L:3-115
Fold
:
Ribosomal L11/L12e N-terminal domain
(53)
Superfamily
:
Ribosomal L11/L12e N-terminal domain
(53)
Family
:
Ribosomal L11/L12e N-terminal domain
(53)
Protein domain
:
Ribosomal protein L11, N-terminal domain
(52)
Deinococcus radiodurans [TaxId: 1299]
(4)
15a
d1xbpg2
G:1-71
Fold
:
Ribosomal protein L22
(105)
Superfamily
:
Ribosomal protein L22
(105)
Family
:
Ribosomal protein L22
(105)
Protein domain
:
Ribosomal protein L22
(105)
Deinococcus radiodurans [TaxId: 1299]
(6)
16a
d1xbpq1
Q:8-134
Fold
:
Ribosomal protein L30p/L7e
(86)
Superfamily
:
Ribosomal protein L30p/L7e
(86)
Family
:
Ribosomal protein L30p/L7e
(86)
Protein domain
:
Prokaryotic ribosomal protein L30
(46)
Deinococcus radiodurans [TaxId: 1299]
(6)
17a
d1xbpx1
X:1-55
Fold
:
Ribosomal protein L6
(90)
Superfamily
:
Ribosomal protein L6
(90)
Family
:
Ribosomal protein L6
(90)
Protein domain
:
Ribosomal protein L6
(90)
Deinococcus radiodurans [TaxId: 1299]
(6)
18a
d1xbpe1
E:83-172
18b
d1xbpe2
E:5-82
Fold
:
Ribosomal proteins S24e, L23 and L15e
(151)
Superfamily
:
Ribosomal proteins S24e, L23 and L15e
(151)
Family
:
L23p
(105)
Protein domain
:
Ribosomal protein L23
(105)
Deinococcus radiodurans [TaxId: 1299]
(8)
19a
d1xbpr1
R:2-94
Fold
:
RL5-like
(90)
Superfamily
:
RL5-like
(90)
Family
:
Ribosomal protein L5
(82)
Protein domain
:
Ribosomal protein L5
(82)
Deinococcus radiodurans [TaxId: 1299]
(6)
20a
d1xbpd1
D:3-179
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Ribonuclease H-like motif
(1424)
Superfamily
:
Translational machinery components
(160)
Family
:
Ribosomal protein L18 and S11
(153)
Protein domain
:
Ribosomal protein L18 (L18p)
(83)
Deinococcus radiodurans [TaxId: 1299]
(6)
21a
d1xbpm1
M:8-111
Fold
:
Ribosomal protein L13
(90)
Superfamily
:
Ribosomal protein L13
(90)
Family
:
Ribosomal protein L13
(90)
Protein domain
:
Ribosomal protein L13
(90)
Deinococcus radiodurans [TaxId: 1299]
(6)
22a
d1xbph1
H:30-171
Fold
:
Ribosomal protein L4
(89)
Superfamily
:
Ribosomal protein L4
(89)
Family
:
Ribosomal protein L4
(89)
Protein domain
:
Ribosomal protein L4
(89)
Deinococcus radiodurans [TaxId: 1299]
(6)
23a
d1xbpc1
C:2-198
Fold
:
Ribosomal proteins L15p and L18e
(126)
Superfamily
:
Ribosomal proteins L15p and L18e
(126)
Family
:
Ribosomal proteins L15p and L18e
(126)
Protein domain
:
Ribosomal protein L15 (L15p)
(86)
Deinococcus radiodurans [TaxId: 1299]
(6)
24a
d1xbpj1
J:4-144
Class
:
Peptides
(792)
Fold
:
Ribosomal protein L34p
(29)
Superfamily
:
Ribosomal protein L34p
(29)
Family
:
Ribosomal protein L34p
(29)
Protein domain
:
Ribosomal protein L34p
(29)
Deinococcus radiodurans [TaxId: 1299]
(6)
25a
d1xbp21
2:1-46
Class
:
Small proteins
(3458)
Fold
:
Ribosomal protein L36
(43)
Superfamily
:
Ribosomal protein L36
(43)
Family
:
Ribosomal protein L36
(43)
Protein domain
:
Ribosomal protein L36
(43)
Deinococcus radiodurans [TaxId: 1299]
(6)
26a
d1xbp41
4:2-36
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Zn-binding ribosomal proteins
(209)
Family
:
Ribosomal protein L32p
(44)
Protein domain
:
Ribosomal protein L32p
(44)
Deinococcus radiodurans [TaxId: 1299]
(6)
27a
d1xbpz1
Z:2-59
Family
:
Ribosomal protein L33p
(24)
Protein domain
:
Ribosomal protein L33p
(24)
Deinococcus radiodurans [TaxId: 1299]
(6)
28a
d1xbp11
1:2-54
[
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]
CATH Domains
(0, 0)
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all CATH domains
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all PFAM domains
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