1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lentzen, G.
Klinck, R.
Matassova, N.
Aboul-Ela, F.
Murchie, A.I.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H5 N O2 S
119.142
n
(2Z)-2-amino-3-sulfanylprop-2-enoic acid
peptide linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C4 H7 N O2
101.104
n
(2Z)-2-AMINOBUT-2-ENOIC ACID
Z-DEHYDROBUTYRINE
peptide linking
C3 H7 N O2 S
121.158
D-CYSTEINE
D-peptide linking
C3 H5 N O2
87.077
n
2-AMINO-ACRYLIC ACID
2,3-DIDEHYDROALANINE
peptide linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C3 H5 N O3
103.077
n
3-hydroxy-2-iminopropanoic acid
peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C12 H13 N O4
235.236
8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
non-polymer
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C6 H13 N O4
163.172
n
(2S,3S,4R)-2-amino-3,4-dihydroxy-3-methylpentanoic acid
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Chem.Biol.
CBOLE2
2050
1074-5521
10
769
10.1016/S1074-5521(03)00173-X
12954336
Structural Basis for Contrasting Activities of Ribosome Binding Thiazole Antibiotics
2003
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
97
491
10.1016/S0092-8674(00)80759-X
10338213
A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
1999
US
Science
SCIEAS
0038
0036-8075
284
1171
10.1126/SCIENCE.284.5417.1171
10325228
Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
1999
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
14980.726
50S RIBOSOMAL PROTEIN L11
1
nat
polymer
1805.985
THIOSTREPTON
1
nat
polymer
18693.145
RNA
RESIDUES 1051-1108
1
nat
polymer
ALANINAMIDE, BRYAMYCIN, THIACTIN
no
no
AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKK
AAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD
AKKVAAQIKLQLPAGKATPAPPVGPALGQHGVNIMEFCKRFNAETADKAGMILPVVITVYEDKSFTFIIKTPPASFLLKK
AAGIEKGSSEPKRKIVGKVTRKQIEEIAKTKMPDLNANSLEAAMKIIEGTAKSMGIEVVD
A
polypeptide(L)
no
yes
(QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)
XIASASCTTCICTCSCSSX
B
polypeptide(L)
no
no
GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
GCUGGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAGUGCGUAACAGCUCACCAGC
C
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
2336
THERMOTOGA MARITIMA
sample
146537
STREPTOMYCES AZUREUS
sample
2336
THERMOTOGA MARITIMA
-6.725
1
19
C
1051
C
1108
6.827
C_G1051:C1108_C
1
-8.819
-0.453
-0.068
0.102
-3.133
1
19
C
1052
C
1107
5.150
C_C1052:G1107_C
2
-17.311
0.367
0.141
-0.289
-6.222
1
20
C
1053
C
1106
9.602
C_U1053:A1106_C
3
-13.374
-0.887
0.105
-0.018
-2.780
1
19
C
1054
C
1105
5.038
C_G1054:C1105_C
4
-8.463
-0.457
0.085
-0.057
-13.474
1
19
C
1055
C
1104
2.434
C_G1055:C1104_C
5
-14.487
0.126
-0.448
-0.229
-17.709
10
11
C
1056
C
1103
-5.174
C_G1056:A1103_C
6
-10.873
6.768
-0.139
-4.215
-11.911
1
19
C
1087
C
1102
4.348
C_G1087:C1102_C
7
-0.941
-0.265
-0.387
0.011
-6.809
1
16
C
1090
C
1101
20.218
C_U1090:U1101_C
8
-5.982
-2.485
0.037
-1.763
-2.787
1
19
C
1091
C
1100
7.170
C_G1091:C1100_C
9
0.730
-0.212
-0.356
-0.084
0.573
1
19
C
1092
C
1099
3.261
C_C1092:G1099_C
10
0.181
-0.037
-0.243
-0.275
-6.476
10
11
C
1093
C
1098
-5.736
C_G1093:A1098_C
11
0.815
6.806
-0.058
-4.083
18.891
2
21
C
1086
C
1082
168.228
C_A1086:U1082_C
12
-6.288
0.232
-0.283
1.405
-1.018
1
20
C
1057
C
1081
8.423
C_A1057:U1081_C
13
-19.131
0.092
0.123
-0.028
-15.671
1
20
C
1058
C
1080
6.802
C_U1058:A1080_C
14
-7.542
-0.197
0.082
-0.108
-7.401
1
19
C
1059
C
1079
-4.126
C_G1059:C1079_C
15
-4.623
-0.131
0.144
-0.257
-2.629
3
23
C
1060
C
1088
-67.855
C_U1060:A1088_C
16
5.058
-0.630
0.653
3.398
1.559
1
19
C
1062
C
1076
-3.633
C_G1062:C1076_C
17
-5.131
-0.273
-0.214
-0.151
-8.395
1
19
C
1063
C
1075
0.132
C_G1063:C1075_C
18
-16.562
-0.297
-0.472
-0.380
-4.999
1
19
C
1064
C
1074
4.496
C_C1064:G1074_C
19
-14.637
0.340
-0.118
-0.331
-9.754
C
1065
C
1073
6.689
C_U1065:A1073_C
20
-5.636
5.606
-0.137
-1.138
2.770
37.165
C
C
1051
1052
12.357
C
C
1108
1107
3.065
7.815
-0.428
-1.249
CC_G1051C1052:G1107C1108_CC
1
-2.682
4.242
36.267
-2.901
0.348
2.401
30.143
C
C
1052
1053
24.763
C
C
1107
1106
3.139
12.505
0.385
-1.138
CC_C1052U1053:A1106G1107_CC
2
-0.239
0.472
27.480
-4.454
-0.784
2.992
33.191
C
C
1053
1054
8.926
C
C
1106
1105
3.216
5.078
0.051
-1.230
CC_U1053G1054:C1105A1106_CC
3
-1.519
2.670
32.776
-2.967
-0.333
2.856
34.487
C
C
1054
1055
19.262
C
C
1105
1104
3.587
11.219
0.195
-1.744
CC_G1054G1055:C1104C1105_CC
4
1.714
-2.943
32.620
-4.708
-0.059
3.486
66.888
C
C
1055
1056
9.838
C
C
1104
1103
3.644
10.803
-0.498
-0.666
CC_G1055G1056:A1103C1104_CC
5
3.331
-3.034
66.035
-1.070
0.595
2.508
38.676
C
C
1056
1087
5.102
C
C
1103
1102
3.246
3.350
-3.406
0.612
CC_G1056G1087:C1102A1103_CC
6
8.328
-12.681
37.659
0.557
6.056
3.591
37.462
C
C
1087
1090
-5.086
C
C
1102
1101
3.388
-3.260
-0.921
-3.414
CC_G1087U1090:U1101C1102_CC
7
2.664
-4.156
37.233
-4.858
1.808
2.926
35.994
C
C
1090
1091
7.745
C
C
1101
1100
3.182
4.771
-0.808
-1.471
CC_U1090G1091:C1100U1101_CC
8
1.729
-2.807
35.646
-3.017
1.539
2.984
29.260
C
C
1091
1092
4.831
C
C
1100
1099
3.184
2.438
-0.024
-2.312
CC_G1091C1092:G1099C1100_CC
9
0.134
-0.266
29.161
-5.076
0.075
3.393
59.686
C
C
1092
1093
5.042
C
C
1099
1098
3.512
5.012
-0.235
-1.285
CC_C1092G1093:A1098G1099_CC
10
2.276
-2.290
59.455
-1.556
0.356
1.215
174.515
C
C
1086
1057
-76.122
C
C
1082
1081
0.742
-150.786
-2.601
-2.575
CC_A1086A1057:U1081U1082_CC
11
78.607
-39.684
113.056
-1.029
1.438
3.086
35.249
C
C
1057
1058
11.930
C
C
1081
1080
3.531
7.170
-0.644
-2.099
CC_A1057U1058:A1080U1081_CC
12
-2.744
4.566
34.429
-4.556
0.646
2.518
29.400
C
C
1058
1059
13.085
C
C
1080
1079
3.114
6.573
-1.017
-1.756
CC_U1058G1059:C1079A1080_CC
13
3.393
-6.755
28.474
-4.695
2.642
-1.670
-179.473
C
C
1059
1060
84.329
C
C
1079
1088
-1.653
-168.644
2.880
-0.799
CC_G1059U1060:A1088C1079_CC
14
-26.651
-13.327
-173.467
0.353
1.448
3.088
36.833
C
C
1062
1063
12.526
C
C
1076
1075
3.516
7.856
-0.429
-1.765
CC_G1062G1063:C1075C1076_CC
15
-1.132
1.804
35.996
-3.883
0.522
3.099
35.470
C
C
1063
1064
3.798
C
C
1075
1074
3.189
2.312
0.878
-1.623
CC_G1063C1064:G1074C1075_CC
16
0.800
-1.315
35.389
-2.990
-1.328
3.297
51.703
C
C
1064
1065
7.547
C
C
1074
1073
3.425
6.551
0.331
-1.004
CC_C1064U1065:A1073G1074_CC
17
6.517
-7.508
50.927
-1.610
0.077
pdbx_database_related
database_PDB_rev
database_PDB_rev_record
entity_poly
pdbx_seq_map_depositor_info
struct_conn
pdbx_nmr_software
repository
Initial release
Atomic model
Database references
Derived calculations
Structure summary
Version format compliance
Other
Database references
Data collection
Derived calculations
Polymer sequence
Data collection
1
0
2003-09-11
1
1
2011-07-13
1
2
2012-11-30
1
3
2017-11-15
2
0
2019-04-24
2
1
2019-08-21
_pdbx_database_related.db_name
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_seq_map_depositor_info.one_letter_code
_struct_conn.pdbx_leaving_atom_flag
_pdbx_nmr_software.name
CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A.
CRYSTAL STRUCTURE OF THIOPEPTIDE THIOSTREPTON
CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A.
SOLUTION STRUCTURE OF THE COMPLEX OF THIOPEPTIDE THIOSTREPTON AND RIBOSOMAL L11-RNA
CRYSTAL STRUCTURE OF NOSIHEPTIDE COMPLEXED WITH THE LARGE RIBOSOMAL SUBUNIT OF DEINOCOCCUS RADIODURANS
CRYSTAL STRUCTURE OF RIBOSOMAL L11-RNA COMPLEXED WITH THE THIOPEPTIDE THIOSTREPTON
CRYSTAL STRUCTURE OF THE RIBOSOMAL PROTEIN L11-RNA COMPLEX
FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E. COLI 70S RIBOSOME
CRYSTAL STRUCTURE OF THE RIBOSOME AT 5.5A RESOLUTIO
FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (EF-G) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUND WITH EF-G,GDP AND FUSIDIC ACID
FITTING OF L11 PROTEIN AND ELONGATION FACTOR G (DOMAIN G'AND V) IN THE CRYO-EM MAP OF E. COLI 70S RIBOSOME BOUNDWITH EF-G AND GMPPCP
FITTING OF L11 PROTEIN IN THE LOW RESOLUTION CRYO-EM MAP OFE.COLI 70S RIBOSOME
COORDINATES OF S12, L11 PROTEINS AND P-TRNA, FROM THE 70S X-RAY STRUCTURE ALIGNED TO THE 70S CRYO-EM MAP OF E. COLIRIBOSOME
COORDINATES OF S12, L11 PROTEINS AND E-SITE TRNA FROM 70S CRYSTAL STRUCTURE SEPARATELY FITTED INTO THE CRYO-EM MAPOF E.COLI 70S.EF-G.GDPNP COMPLEX. THE COORDINATESORIGINALLY FROM THE E-SITE TRNA WERE FITTED IN THEPOSITION OF THE HYBRID P /E-SITE TRNA.
SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-EM MAP OF THE LARGE 50S SUBUNIT AT 7.5 A.
PDBE
Y
PDBE
2003-08-08
REL
THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES
CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A
NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO
ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING
THIAZOLES, THIAZOLINES AND OXAZOLES.
HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES)
GROUP: 1
NAME: THIOSTREPTON
CHAIN: B
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18
DESCRIPTION: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE,
CONSISTING OF FOUR THIAZOLES ONE THIAZOLINE
ONE PIPERIDEINE RINGS.
A MODIFIED QUINOLINE LINKED TO MAIN-CHAIN
RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12.
THE OBSERVED C-TERMINAL AMINO GROUP NH2(18) IS
LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED
REMNANT OF A SER C-TERMINAL RESIDUE.
Antibiotic
Thiostrepton is a hetrocyclic thiopeptide belonging to the
thiocillin family, consisting of four thiazole, one thiozoline and one
piperideine rings. A modified quinoline linked to main-chain residue 1
and side-chain of residue 12. Post translational maturation of
thiazole and oxazole containing antibiotics involves the enzymic
condensation of a Cys or Ser with the alpha-carbonyl of the preceding
amino acid to form a thioether or ether bond, then dehydration to form
a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline
ring are dehydrogenated to form thiazole or oxazole rings. the
pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair
usually separated by 7 or 8 residues along the peptide chain. The Ser
residues are dehydrated to didehydroalanines, then bonded between
their beta carbons. The alpha carbonyl of the Cys condenses with alpha
carbon of the first Ser to form a pyridinyl ring. The ring may be
mutiply dehydrogenated to form a pyridine ring with loss of the amino
nitrogen of the first Ser. The amidation of Ser-17 probably does not
occur by the same mechanism, oxidative cleavage of glycine, as in
eukaryotes.
THIOSTREPTON
Thiopeptide
BEST OVERALL DOCKING SCORE AND LEAST RESTRAINT VIOLATION. THE NOES INCLUDED IN THE RESTRAINTED MODELING WERE OBTAINED FROM A FILTERED NOESY EXPERIMENT ON A COMPLEX OF UNLABELED THIOSTREPTON WITH THE RNA. AS ALL INTERNAL COORDINATES WERE HELD RIGID ACCORDING TO THE X-RAY STRUCTURES, ONLY INTERMOLECULAR NOES WERE INCLUDED. ASSIGNMENTS FOR RNA WERE CHOSEN FROM AN ITERATIVE DOCKING PROCESS (SEE LENTZEN ET AL AND MANUSCRIPT TO BE PUBLISHED)
LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE
1
NOESY
100 MM NACL, 5 MM MGCL2
6.2
pH
1
atm
303
K
THE COORDINATES OF THE PROTEIN, RNA AND THE ANTIBIOTIC WERE HELD RIGID DURING REFINEMENT. THE COORDINATES OF THE RIBOSOMAL L11 (CHAIN A) AND THE RNA (CHAIN C) WERE FROM PDB ENTRY 1MMS. THE COORDINATES OF THE ANTIBIOTIC THIOSTREPTON (CHAIN B) WERE FROM PDB ENTRY 1E9W. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION.
DOCKING/MODELING
DAVID MORLEY
refinement
rDOCK
600
Bruker
DRX
n
1
2
A
n
2
3
A
n
3
4
A
n
4
5
A
n
5
6
A
n
6
7
A
GLN
8
n
7
GLN
8
A
ILE
9
n
8
ILE
9
A
LYS
10
n
9
LYS
10
A
LEU
11
n
10
LEU
11
A
GLN
12
n
11
GLN
12
A
LEU
13
n
12
LEU
13
A
PRO
14
n
13
PRO
14
A
ALA
15
n
14
ALA
15
A
GLY
16
n
15
GLY
16
A
LYS
17
n
16
LYS
17
A
ALA
18
n
17
ALA
18
A
THR
19
n
18
THR
19
A
PRO
20
n
19
PRO
20
A
ALA
21
n
20
ALA
21
A
PRO
22
n
21
PRO
22
A
PRO
23
n
22
PRO
23
A
VAL
24
n
23
VAL
24
A
GLY
25
n
24
GLY
25
A
PRO
26
n
25
PRO
26
A
ALA
27
n
26
ALA
27
A
LEU
28
n
27
LEU
28
A
GLY
29
n
28
GLY
29
A
GLN
30
n
29
GLN
30
A
HIS
31
n
30
HIS
31
A
GLY
32
n
31
GLY
32
A
VAL
33
n
32
VAL
33
A
ASN
34
n
33
ASN
34
A
ILE
35
n
34
ILE
35
A
MET
36
n
35
MET
36
A
GLU
37
n
36
GLU
37
A
PHE
38
n
37
PHE
38
A
CYS
39
n
38
CYS
39
A
LYS
40
n
39
LYS
40
A
ARG
41
n
40
ARG
41
A
PHE
42
n
41
PHE
42
A
ASN
43
n
42
ASN
43
A
ALA
44
n
43
ALA
44
A
GLU
45
n
44
GLU
45
A
THR
46
n
45
THR
46
A
ALA
47
n
46
ALA
47
A
ASP
48
n
47
ASP
48
A
LYS
49
n
48
LYS
49
A
ALA
50
n
49
ALA
50
A
GLY
51
n
50
GLY
51
A
MET
52
n
51
MET
52
A
ILE
53
n
52
ILE
53
A
LEU
54
n
53
LEU
54
A
PRO
55
n
54
PRO
55
A
VAL
56
n
55
VAL
56
A
VAL
57
n
56
VAL
57
A
ILE
58
n
57
ILE
58
A
THR
59
n
58
THR
59
A
VAL
60
n
59
VAL
60
A
TYR
61
n
60
TYR
61
A
GLU
62
n
61
GLU
62
A
ASP
63
n
62
ASP
63
A
LYS
64
n
63
LYS
64
A
SER
65
n
64
SER
65
A
PHE
66
n
65
PHE
66
A
THR
67
n
66
THR
67
A
PHE
68
n
67
PHE
68
A
ILE
69
n
68
ILE
69
A
ILE
70
n
69
ILE
70
A
LYS
71
n
70
LYS
71
A
THR
72
n
71
THR
72
A
PRO
73
n
72
PRO
73
A
PRO
74
n
73
PRO
74
A
ALA
75
n
74
ALA
75
A
SER
76
n
75
SER
76
A
PHE
77
n
76
PHE
77
A
LEU
78
n
77
LEU
78
A
LEU
79
n
78
LEU
79
A
LYS
80
n
79
LYS
80
A
LYS
81
n
80
LYS
81
A
ALA
82
n
81
ALA
82
A
ALA
83
n
82
ALA
83
A
GLY
84
n
83
GLY
84
A
ILE
85
n
84
ILE
85
A
GLU
86
n
85
GLU
86
A
LYS
87
n
86
LYS
87
A
GLY
88
n
87
GLY
88
A
SER
89
n
88
SER
89
A
SER
90
n
89
SER
90
A
GLU
91
n
90
GLU
91
A
PRO
92
n
91
PRO
92
A
LYS
93
n
92
LYS
93
A
ARG
94
n
93
ARG
94
A
LYS
95
n
94
LYS
95
A
ILE
96
n
95
ILE
96
A
VAL
97
n
96
VAL
97
A
GLY
98
n
97
GLY
98
A
LYS
99
n
98
LYS
99
A
VAL
100
n
99
VAL
100
A
THR
101
n
100
THR
101
A
ARG
102
n
101
ARG
102
A
LYS
103
n
102
LYS
103
A
GLN
104
n
103
GLN
104
A
ILE
105
n
104
ILE
105
A
GLU
106
n
105
GLU
106
A
GLU
107
n
106
GLU
107
A
ILE
108
n
107
ILE
108
A
ALA
109
n
108
ALA
109
A
LYS
110
n
109
LYS
110
A
THR
111
n
110
THR
111
A
LYS
112
n
111
LYS
112
A
MET
113
n
112
MET
113
A
PRO
114
n
113
PRO
114
A
ASP
115
n
114
ASP
115
A
LEU
116
n
115
LEU
116
A
ASN
117
n
116
ASN
117
A
ALA
118
n
117
ALA
118
A
ASN
119
n
118
ASN
119
A
SER
120
n
119
SER
120
A
LEU
121
n
120
LEU
121
A
GLU
122
n
121
GLU
122
A
ALA
123
n
122
ALA
123
A
ALA
124
n
123
ALA
124
A
MET
125
n
124
MET
125
A
LYS
126
n
125
LYS
126
A
ILE
127
n
126
ILE
127
A
ILE
128
n
127
ILE
128
A
GLU
129
n
128
GLU
129
A
GLY
130
n
129
GLY
130
A
THR
131
n
130
THR
131
A
ALA
132
n
131
ALA
132
A
LYS
133
n
132
LYS
133
A
SER
134
n
133
SER
134
A
MET
135
n
134
MET
135
A
GLY
136
n
135
GLY
136
A
ILE
137
n
136
ILE
137
A
GLU
138
n
137
GLU
138
A
VAL
139
n
138
VAL
139
A
VAL
140
n
139
VAL
140
A
n
140
141
A
QUA
0
n
1
QUA
0
B
ILE
1
n
2
ILE
1
B
ALA
2
n
3
ALA
2
B
DHA
3
n
4
DHA
3
B
ALA
4
n
5
ALA
4
B
SER
5
n
6
SER
5
B
BB9
6
n
7
BB9
6
B
THR
7
n
8
THR
7
B
DBU
8
n
9
DBU
8
B
DCY
9
n
10
DCY
9
B
TS9
10
n
11
TS9
10
B
BB9
11
n
12
BB9
11
B
THR
12
n
13
THR
12
B
BB9
13
n
14
BB9
13
B
MH6
14
n
15
MH6
14
B
BB9
15
n
16
BB9
15
B
DHA
16
n
17
DHA
16
B
DHA
17
n
18
DHA
17
B
NH2
18
n
19
NH2
18
B
G
1051
n
1
G
1051
C
C
1052
n
2
C
1052
C
U
1053
n
3
U
1053
C
G
1054
n
4
G
1054
C
G
1055
n
5
G
1055
C
G
1056
n
6
G
1056
C
A
1057
n
7
A
1057
C
U
1058
n
8
U
1058
C
G
1059
n
9
G
1059
C
U
1060
n
10
U
1060
C
U
1061
n
11
U
1061
C
G
1062
n
12
G
1062
C
G
1063
n
13
G
1063
C
C
1064
n
14
C
1064
C
U
1065
n
15
U
1065
C
U
1066
n
16
U
1066
C
A
1067
n
17
A
1067
C
G
1068
n
18
G
1068
C
A
1069
n
19
A
1069
C
A
1070
n
20
A
1070
C
G
1071
n
21
G
1071
C
C
1072
n
22
C
1072
C
A
1073
n
23
A
1073
C
G
1074
n
24
G
1074
C
C
1075
n
25
C
1075
C
C
1076
n
26
C
1076
C
A
1077
n
27
A
1077
C
U
1078
n
28
U
1078
C
C
1079
n
29
C
1079
C
A
1080
n
30
A
1080
C
U
1081
n
31
U
1081
C
U
1082
n
32
U
1082
C
U
1083
n
33
U
1083
C
A
1084
n
34
A
1084
C
A
1085
n
35
A
1085
C
A
1086
n
36
A
1086
C
G
1087
n
37
G
1087
C
A
1088
n
38
A
1088
C
G
1089
n
39
G
1089
C
U
1090
n
40
U
1090
C
G
1091
n
41
G
1091
C
C
1092
n
42
C
1092
C
G
1093
n
43
G
1093
C
U
1094
n
44
U
1094
C
A
1095
n
45
A
1095
C
A
1096
n
46
A
1096
C
C
1097
n
47
C
1097
C
A
1098
n
48
A
1098
C
G
1099
n
49
G
1099
C
C
1100
n
50
C
1100
C
U
1101
n
51
U
1101
C
C
1102
n
52
C
1102
C
A
1103
n
53
A
1103
C
C
1104
n
54
C
1104
C
C
1105
n
55
C
1105
C
A
1106
n
56
A
1106
C
G
1107
n
57
G
1107
C
C
1108
n
58
C
1108
C
author_defined_assembly
3
trimeric
B
DHA
3
2-AMINO-ACRYLIC ACID
B
DHA
4
SER
B
BB9
6
B
BB9
7
CYS
B
DBU
8
(2Z)-2-AMINOBUT-2-ENOIC ACID
B
DBU
9
THR
B
TS9
10
B
TS9
11
ILE
B
BB9
11
B
BB9
12
CYS
B
BB9
13
B
BB9
14
CYS
B
MH6
14
3-HYDROXY-2-IMINOPROPANOIC ACID
B
MH6
15
SER
B
BB9
15
B
BB9
16
CYS
B
DHA
16
2-AMINO-ACRYLIC ACID
B
DHA
17
SER
B
DHA
17
2-AMINO-ACRYLIC ACID
B
DHA
18
SER
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
LEU
13
A
N
LEU
12
A
O
LEU
54
A
O
LEU
53
A
N
THR
59
A
N
THR
58
A
O
THR
67
A
O
THR
66
A
N
VAL
100
A
N
VAL
99
A
O
GLU
138
A
O
GLU
137
1
A
ALA
2
A
ALA
1
1
Y
1
A
LYS
3
A
LYS
2
1
Y
1
A
LYS
4
A
LYS
3
1
Y
1
A
VAL
5
A
VAL
4
1
Y
1
A
ALA
6
A
ALA
5
1
Y
1
A
ALA
7
A
ALA
6
1
Y
1
A
ASP
141
A
ASP
140
1
Y
1
C
A
1069
0.061
SIDE CHAIN
1
B
B
C
N
BB9
MH6
13
14
0.138
0.023
1.336
1.474
Y
1
A
ALA
15
-38.18
-99.29
1
A
LYS
17
-176.59
140.91
1
A
THR
19
95.17
-25.33
1
A
VAL
24
-94.06
-92.82
1
A
PRO
26
-28.71
-52.70
1
A
ALA
27
-39.55
-89.24
1
A
ILE
35
-27.29
-73.68
1
A
GLU
62
-34.81
-34.92
1
A
LYS
64
68.48
-9.28
1
A
LYS
93
75.48
-42.99
1
B
SER
5
71.83
80.85
1
B
DCY
9
-147.29
-14.72
1
B
TS9
10
-107.46
-65.50
50S RIBOSOMAL PROTEIN L11, THIOSTREPTON
MINIMIZED AVERAGE
Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA
1
N
N
2
N
N
3
N
N
A
GLY
25
A
GLY
24
HELX_P
A
GLN
30
A
GLN
29
1
1
6
A
ASN
34
A
ASN
33
HELX_P
A
THR
46
A
THR
45
1
2
13
A
PRO
74
A
PRO
73
HELX_P
A
GLY
84
A
GLY
83
1
3
11
A
ARG
102
A
ARG
101
HELX_P
A
MET
113
A
MET
112
1
4
12
A
PRO
114
A
PRO
113
HELX_P
A
LEU
116
A
LEU
115
5
5
3
A
SER
120
A
SER
119
HELX_P
A
LYS
133
A
LYS
132
1
6
14
covale
1.329
one
B
QUA
0
B
C11
QUA
1
1_555
B
THR
12
B
OG1
THR
13
1_555
covale
1.499
one
B
QUA
0
B
C7
QUA
1
1_555
B
ILE
1
B
N
ILE
2
1_555
covale
1.383
both
B
ALA
2
B
C
ALA
3
1_555
B
DHA
3
B
N
DHA
4
1_555
covale
1.348
both
B
DHA
3
B
C
DHA
4
1_555
B
ALA
4
B
N
ALA
5
1_555
covale
1.752
one
B
SER
5
B
C
SER
6
1_555
B
BB9
6
B
SG
BB9
7
1_555
covale
1.575
one
B
SER
5
B
CA
SER
6
1_555
B
BB9
13
B
C
BB9
14
1_555
covale
1.524
one
B
SER
5
B
CB
SER
6
1_555
B
MH6
14
B
CB
MH6
15
1_555
covale
1.306
both
B
SER
5
B
C
SER
6
1_555
B
BB9
6
B
N
BB9
7
1_555
covale
1.323
both
B
BB9
6
B
C
BB9
7
1_555
B
THR
7
B
N
THR
8
1_555
covale
1.352
both
B
THR
7
B
C
THR
8
1_555
B
DBU
8
B
N
DBU
9
1_555
covale
1.294
both
B
DBU
8
B
C
DBU
9
1_555
B
DCY
9
B
N
DCY
10
1_555
covale
1.749
one
B
DBU
8
B
C
DBU
9
1_555
B
DCY
9
B
SG
DCY
10
1_555
covale
1.328
both
B
DCY
9
B
C
DCY
10
1_555
B
TS9
10
B
N
TS9
11
1_555
covale
1.750
one
B
TS9
10
B
C
TS9
11
1_555
B
BB9
11
B
SG
BB9
12
1_555
covale
1.279
both
B
TS9
10
B
C
TS9
11
1_555
B
BB9
11
B
N
BB9
12
1_555
covale
1.359
both
B
BB9
11
B
C
BB9
12
1_555
B
THR
12
B
N
THR
13
1_555
covale
1.708
one
B
THR
12
B
C
THR
13
1_555
B
BB9
13
B
SG
BB9
14
1_555
covale
1.292
both
B
THR
12
B
C
THR
13
1_555
B
BB9
13
B
N
BB9
14
1_555
covale
1.474
both
B
BB9
13
B
C
BB9
14
1_555
B
MH6
14
B
N
MH6
15
1_555
covale
1.650
one
B
MH6
14
B
C
MH6
15
1_555
B
BB9
15
B
SG
BB9
16
1_555
covale
1.301
both
B
MH6
14
B
C
MH6
15
1_555
B
BB9
15
B
N
BB9
16
1_555
covale
1.380
both
B
BB9
15
B
C
BB9
16
1_555
B
DHA
16
B
N
DHA
17
1_555
covale
1.229
both
B
DHA
16
B
C
DHA
17
1_555
B
DHA
17
B
N
DHA
18
1_555
covale
1.350
both
B
DHA
17
B
C
DHA
18
1_555
B
NH2
18
B
N
NH2
19
1_555
hydrog
WATSON-CRICK
C
G
1051
C
N1
G
1
1_555
C
C
1108
C
N3
C
58
1_555
hydrog
WATSON-CRICK
C
G
1051
C
N2
G
1
1_555
C
C
1108
C
O2
C
58
1_555
hydrog
WATSON-CRICK
C
G
1051
C
O6
G
1
1_555
C
C
1108
C
N4
C
58
1_555
hydrog
WATSON-CRICK
C
C
1052
C
N3
C
2
1_555
C
G
1107
C
N1
G
57
1_555
hydrog
WATSON-CRICK
C
C
1052
C
N4
C
2
1_555
C
G
1107
C
O6
G
57
1_555
hydrog
WATSON-CRICK
C
C
1052
C
O2
C
2
1_555
C
G
1107
C
N2
G
57
1_555
hydrog
WATSON-CRICK
C
U
1053
C
N3
U
3
1_555
C
A
1106
C
N1
A
56
1_555
hydrog
WATSON-CRICK
C
U
1053
C
O4
U
3
1_555
C
A
1106
C
N6
A
56
1_555
hydrog
WATSON-CRICK
C
G
1054
C
N1
G
4
1_555
C
C
1105
C
N3
C
55
1_555
hydrog
WATSON-CRICK
C
G
1054
C
N2
G
4
1_555
C
C
1105
C
O2
C
55
1_555
hydrog
WATSON-CRICK
C
G
1054
C
O6
G
4
1_555
C
C
1105
C
N4
C
55
1_555
hydrog
G-A MISPAIR
C
G
1055
C
N2
G
5
1_555
C
A
1085
C
N3
A
35
1_555
hydrog
WATSON-CRICK
C
G
1055
C
N1
G
5
1_555
C
C
1104
C
N3
C
54
1_555
hydrog
WATSON-CRICK
C
G
1055
C
N2
G
5
1_555
C
C
1104
C
O2
C
54
1_555
hydrog
WATSON-CRICK
C
G
1055
C
O6
G
5
1_555
C
C
1104
C
N4
C
54
1_555
hydrog
TYPE_11_PAIR
C
G
1056
C
N2
G
6
1_555
C
A
1103
C
N7
A
53
1_555
hydrog
TYPE_11_PAIR
C
G
1056
C
N3
G
6
1_555
C
A
1103
C
N6
A
53
1_555
hydrog
WATSON-CRICK
C
A
1057
C
N1
A
7
1_555
C
U
1081
C
N3
U
31
1_555
hydrog
WATSON-CRICK
C
A
1057
C
N6
A
7
1_555
C
U
1081
C
O4
U
31
1_555
hydrog
WATSON-CRICK
C
U
1058
C
N3
U
8
1_555
C
A
1080
C
N1
A
30
1_555
hydrog
WATSON-CRICK
C
U
1058
C
O4
U
8
1_555
C
A
1080
C
N6
A
30
1_555
hydrog
WATSON-CRICK
C
G
1059
C
N1
G
9
1_555
C
C
1079
C
N3
C
29
1_555
hydrog
WATSON-CRICK
C
G
1059
C
N2
G
9
1_555
C
C
1079
C
O2
C
29
1_555
hydrog
WATSON-CRICK
C
G
1059
C
O6
G
9
1_555
C
C
1079
C
N4
C
29
1_555
hydrog
HOOGSTEEN
C
U
1060
C
N3
U
10
1_555
C
A
1088
C
N7
A
38
1_555
hydrog
HOOGSTEEN
C
U
1060
C
O4
U
10
1_555
C
A
1088
C
N6
A
38
1_555
hydrog
WATSON-CRICK
C
G
1062
C
N1
G
12
1_555
C
C
1076
C
N3
C
26
1_555
hydrog
WATSON-CRICK
C
G
1062
C
N2
G
12
1_555
C
C
1076
C
O2
C
26
1_555
hydrog
WATSON-CRICK
C
G
1062
C
O6
G
12
1_555
C
C
1076
C
N4
C
26
1_555
hydrog
WATSON-CRICK
C
G
1063
C
N1
G
13
1_555
C
C
1075
C
N3
C
25
1_555
hydrog
WATSON-CRICK
C
G
1063
C
N2
G
13
1_555
C
C
1075
C
O2
C
25
1_555
hydrog
WATSON-CRICK
C
G
1063
C
O6
G
13
1_555
C
C
1075
C
N4
C
25
1_555
hydrog
WATSON-CRICK
C
C
1064
C
N3
C
14
1_555
C
G
1074
C
N1
G
24
1_555
hydrog
WATSON-CRICK
C
C
1064
C
N4
C
14
1_555
C
G
1074
C
O6
G
24
1_555
hydrog
WATSON-CRICK
C
C
1064
C
O2
C
14
1_555
C
G
1074
C
N2
G
24
1_555
hydrog
U-A PAIR
C
U
1065
C
O2
U
15
1_555
C
A
1073
C
N6
A
23
1_555
hydrog
TYPE_6_PAIR
C
G
1071
C
N1
G
21
1_555
C
G
1091
C
O6
G
41
1_555
hydrog
TYPE_6_PAIR
C
G
1071
C
N2
G
21
1_555
C
G
1091
C
N7
G
41
1_555
hydrog
G-C PAIR
C
G
1071
C
O6
G
21
1_555
C
C
1100
C
N4
C
50
1_555
hydrog
C-C MISPAIR
C
C
1072
C
N3
C
22
1_555
C
C
1092
C
N4
C
42
1_555
hydrog
C-G PAIR
C
C
1072
C
N4
C
22
1_555
C
G
1099
C
O6
G
49
1_555
hydrog
REVERSED WATSON-CRICK
C
U
1082
C
N3
U
32
1_555
C
A
1086
C
N1
A
36
1_555
hydrog
REVERSED WATSON-CRICK
C
U
1082
C
O2
U
32
1_555
C
A
1086
C
N6
A
36
1_555
hydrog
WATSON-CRICK
C
G
1087
C
N1
G
37
1_555
C
C
1102
C
N3
C
52
1_555
hydrog
WATSON-CRICK
C
G
1087
C
N2
G
37
1_555
C
C
1102
C
O2
C
52
1_555
hydrog
WATSON-CRICK
C
G
1087
C
O6
G
37
1_555
C
C
1102
C
N4
C
52
1_555
hydrog
G-U MISPAIR
C
G
1089
C
N2
G
39
1_555
C
U
1101
C
O4
U
51
1_555
hydrog
TYPE_16_PAIR
C
U
1090
C
N3
U
40
1_555
C
U
1101
C
O2
U
51
1_555
hydrog
TYPE_16_PAIR
C
U
1090
C
O4
U
40
1_555
C
U
1101
C
N3
U
51
1_555
hydrog
WATSON-CRICK
C
G
1091
C
N1
G
41
1_555
C
C
1100
C
N3
C
50
1_555
hydrog
WATSON-CRICK
C
G
1091
C
N2
G
41
1_555
C
C
1100
C
O2
C
50
1_555
hydrog
WATSON-CRICK
C
G
1091
C
O6
G
41
1_555
C
C
1100
C
N4
C
50
1_555
hydrog
WATSON-CRICK
C
C
1092
C
N3
C
42
1_555
C
G
1099
C
N1
G
49
1_555
hydrog
WATSON-CRICK
C
C
1092
C
N4
C
42
1_555
C
G
1099
C
O6
G
49
1_555
hydrog
WATSON-CRICK
C
C
1092
C
O2
C
42
1_555
C
G
1099
C
N2
G
49
1_555
hydrog
TYPE_11_PAIR
C
G
1093
C
N2
G
43
1_555
C
A
1098
C
N7
A
48
1_555
hydrog
TYPE_11_PAIR
C
G
1093
C
N3
G
43
1_555
C
A
1098
C
N6
A
48
1_555
RIBOSOME/ANTIBIOTIC
RIBOSOME-ANTIBIOTIC COMPLEX, THIOPEPTIDE, ANTIBACTERIAL, THIAZOLE, OXAZOLE, RIBOSOME, L11, TRANSLATION INHIBITION
RL11_THEMA
UNP
1
P29395
THCL_STRAJ
UNP
2
P0C8P8
1OLN
PDB
3
1OLN
2
141
1OLN
2
141
P29395
A
1
1
140
1
17
1OLN
1
17
P0C8P8
B
2
2
18
1051
1108
1OLN
1051
1108
1OLN
C
3
1
58
3
2
anti-parallel
anti-parallel
parallel
A
ILE
9
A
ILE
8
A
PRO
14
A
PRO
13
A
ILE
53
A
ILE
52
A
VAL
60
A
VAL
59
A
PHE
66
A
PHE
65
A
ILE
70
A
ILE
69
A
GLY
98
A
GLY
97
A
THR
101
A
THR
100
A
ILE
137
A
ILE
136
A
VAL
140
A
VAL
139
BINDING SITE FOR CHAIN B OF THIOSTREPTON
Software
4
A
PRO
22
A
PRO
21
4
1_555
C
A
1067
C
A
17
4
1_555
C
G
1068
C
G
18
4
1_555
C
A
1095
C
A
45
4
1_555
1
P 1