0.037627
0.000000
0.000000
0.000000
0.037627
0.000000
0.000000
0.000000
0.036448
0.00000
0.00000
0.00000
Bond, C.S.
Shaw, M.P.
Alphey, M.S.
Hunter, W.N.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
26.577
26.577
27.436
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C3 H5 N O2 S
119.142
n
(2Z)-2-amino-3-sulfanylprop-2-enoic acid
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
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
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
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
57
755
10.1107/S0907444901003134
11320328
Structure of the Macrocycle Thiostrepton Solved Using the Anomalous Dispersive Contribution from Sulfur
2001
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
CCD
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.73
1.0
BM14
ESRF
0.73
SYNCHROTRON
ESRF BEAMLINE BM14
1805.985
THIOSTREPTON
1
nat
polymer
18.015
water
4
nat
water
ALANINAMIDE, BRYAMYCIN, THIACTIN
no
yes
(QUA)IA(DHA)AS(BB9)T(DBU)(DCY)(TS9)(BB9)T(BB9)(MH6)(BB9)(DHA)(DHA)(NH2)
XIASASCTTCICTCSCSSX
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
CALBIOCHEM
sample
146537
STREPTOMYCES AZUREUS
1
1.46
14.8
7.00
1ML 15.38MG/ML THIOSTREPTON IN CHLOROFORM_ISOAMYL ALCOHOL + 100 MICROL GLYCEROL + 200 MICROL ETHANOL. BATCH METHOD, pH 7.00
database_PDB_rev
database_PDB_rev_record
entity_poly
pdbx_database_proc
pdbx_database_status
pdbx_seq_map_depositor_info
struct_conn
refine
repository
Initial release
Atomic model
Database references
Derived calculations
Structure summary
Version format compliance
Other
Data collection
Derived calculations
Other
Polymer sequence
Data collection
Refinement description
1
0
2001-03-23
1
1
2011-07-13
1
2
2012-11-30
2
0
2019-04-24
2
1
2019-05-22
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_database_status.recvd_author_approval
_pdbx_seq_map_depositor_info.one_letter_code
_struct_conn.pdbx_leaving_atom_flag
_refine.pdbx_ls_cross_valid_method
CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-MGGDP COMPLEXED WITH THE THIOPEPTIDE GE2270A.
SOLUTION STRUCTURE OF THIOPEPTIDE THIOSTREPTON BINDING TO L11 SUBSTRATE FROM 50S RIBOSOMAL RNA
CRYSTAL STRUCTURE OF THE ELONGATION FACTOR EF-TU-GNP COMPLEXED WITH THIOPEPTIDE GE2270A.
SOLUTION STRUCTURE OF THE COMPLEX OF THE 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
PDBE
Y
PDBE
2000-10-27
REL
HOH
water
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: A
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18
DESCRIPTION: THIOSTREPTON IS A HETROCYCLIC THIOPEPTIDE,
CONSISTING OF FOUR THIAZOLES ONE THIOZOLINE
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
HOH
2001
2
HOH
HOH
2001
A
HOH
2002
2
HOH
HOH
2002
A
HOH
2003
2
HOH
HOH
2003
A
HOH
2004
2
HOH
HOH
2004
A
QUA
0
n
1
QUA
0
A
ILE
1
n
2
ILE
1
A
ALA
2
n
3
ALA
2
A
DHA
3
n
4
DHA
3
A
ALA
4
n
5
ALA
4
A
SER
5
n
6
SER
5
A
BB9
6
n
7
BB9
6
A
THR
7
n
8
THR
7
A
DBU
8
n
9
DBU
8
A
DCY
9
n
10
DCY
9
A
TS9
10
n
11
TS9
10
A
BB9
11
n
12
BB9
11
A
THR
12
n
13
THR
12
A
BB9
13
n
14
BB9
13
A
MH6
14
n
15
MH6
14
A
BB9
15
n
16
BB9
15
A
DHA
16
n
17
DHA
16
A
DHA
17
n
18
DHA
17
A
NH2
18
n
19
NH2
18
A
0.1069
0.1122
0.1071
0.1124
0.1362
0.1423
755
825
9.8
9.8
7729
software_defined_assembly
PISA
1
monomeric
A
DHA
3
2-AMINO-ACRYLIC ACID
A
DHA
4
SER
A
BB9
6
A
BB9
7
CYS
A
DBU
8
(2Z)-2-AMINOBUT-2-ENOIC ACID
A
DBU
9
THR
A
TS9
10
A
TS9
11
ILE
A
BB9
11
A
BB9
12
CYS
A
BB9
13
A
BB9
14
CYS
A
MH6
14
3-HYDROXY-2-IMINOPROPANOIC ACID
A
MH6
15
SER
A
BB9
15
A
BB9
16
CYS
A
DHA
16
2-AMINO-ACRYLIC ACID
A
DHA
17
SER
A
DHA
17
2-AMINO-ACRYLIC ACID
A
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
1
A
HOH
2001
B
HOH
1
A
HOH
2002
B
HOH
1
A
A
C
N
BB9
MH6
13
14
0.139
0.023
1.336
1.475
Y
1
A
SER
5
71.84
80.87
1
A
DCY
9
-147.29
-14.74
1
A
TS9
10
-107.46
-65.52
0.1423
0.1122
0.1124
1.02
50.00
1057
825
8391
1023
9.8
96.7
RANDOM
1
FREE R-VALUE
0.0
MOLECULAR REPLACEMENT
SEE REFERENCE
RESIDUE 16 RESTRAINED USING GEOMETRY DERIVED FROM CSD (SEE REFERENCE)
ENGH AND HUBER
MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
0
0.00
115.33
1.02
50.00
4
118
0
0
114
0.019
0.047
0.000
0.0001
0.000
0.000
0.051
0.007
0.037
0.000
1.020
50.000
1E9W
5232
0.03300
1
33.8000
4.300
96.7
0.15200
1.02
1.04
5.400
1
74.6
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
phasing
SHELX
THIOSTREPTON
Structure of the macrocycle thiostrepton solved using the anomalous dispersive contribution from sulfur
1
N
N
2
N
N
covale
1.329
one
A
QUA
0
A
C11
QUA
1
1_555
A
THR
12
A
OG1
THR
13
1_555
covale
1.499
one
A
QUA
0
A
C7
QUA
1
1_555
A
ILE
1
A
N
ILE
2
1_555
covale
1.383
both
A
ALA
2
A
C
ALA
3
1_555
A
DHA
3
A
N
DHA
4
1_555
covale
1.348
both
A
DHA
3
A
C
DHA
4
1_555
A
ALA
4
A
N
ALA
5
1_555
covale
1.752
one
A
SER
5
A
C
SER
6
1_555
A
BB9
6
A
SG
BB9
7
1_555
covale
1.575
one
A
SER
5
A
CA
SER
6
1_555
A
BB9
13
A
C
BB9
14
1_555
covale
1.523
one
A
SER
5
A
CB
SER
6
1_555
A
MH6
14
A
CB
MH6
15
1_555
covale
1.305
both
A
SER
5
A
C
SER
6
1_555
A
BB9
6
A
N
BB9
7
1_555
covale
1.322
both
A
BB9
6
A
C
BB9
7
1_555
A
THR
7
A
N
THR
8
1_555
covale
1.353
both
A
THR
7
A
C
THR
8
1_555
A
DBU
8
A
N
DBU
9
1_555
covale
1.750
one
A
DBU
8
A
C
DBU
9
1_555
A
DCY
9
A
SG
DCY
10
1_555
covale
1.293
both
A
DBU
8
A
C
DBU
9
1_555
A
DCY
9
A
N
DCY
10
1_555
covale
1.328
both
A
DCY
9
A
C
DCY
10
1_555
A
TS9
10
A
N
TS9
11
1_555
covale
1.750
one
A
TS9
10
A
C
TS9
11
1_555
A
BB9
11
A
SG
BB9
12
1_555
covale
1.279
both
A
TS9
10
A
C
TS9
11
1_555
A
BB9
11
A
N
BB9
12
1_555
covale
1.359
both
A
BB9
11
A
C
BB9
12
1_555
A
THR
12
A
N
THR
13
1_555
covale
1.709
one
A
THR
12
A
C
THR
13
1_555
A
BB9
13
A
SG
BB9
14
1_555
covale
1.292
both
A
THR
12
A
C
THR
13
1_555
A
BB9
13
A
N
BB9
14
1_555
covale
1.475
both
A
BB9
13
A
C
BB9
14
1_555
A
MH6
14
A
N
MH6
15
1_555
covale
1.650
one
A
MH6
14
A
C
MH6
15
1_555
A
BB9
15
A
SG
BB9
16
1_555
covale
1.300
both
A
MH6
14
A
C
MH6
15
1_555
A
BB9
15
A
N
BB9
16
1_555
covale
1.380
both
A
BB9
15
A
C
BB9
16
1_555
A
DHA
16
A
N
DHA
17
1_555
covale
1.229
both
A
DHA
16
A
C
DHA
17
1_555
A
DHA
17
A
N
DHA
18
1_555
covale
1.350
both
A
DHA
17
A
C
DHA
18
1_555
A
NH2
18
A
N
NH2
19
1_555
ANTIBIOTIC
ANTIBIOTIC, THIOPEPTIDE, ANTIBACTERIAL, THIAZOLE, THIAZOLINE, OXAZOLE, RIBOSOME, TRANSLATION INHIBITION
THCL_STRAJ
UNP
1
P0C8P8
1
17
1E9W
1
17
P0C8P8
A
1
2
18
BINDING SITE FOR RESIDUE QUA A 0
Software
15
BINDING SITE FOR RESIDUE NH2 A 18
Software
3
BINDING SITE FOR CHAIN A OF THIOSTREPTON
Software
11
A
ILE
1
A
ILE
2
15
1_555
A
ALA
2
A
ALA
3
15
1_555
A
DHA
3
A
DHA
4
15
1_555
A
DHA
3
A
DHA
4
15
3_554
A
ALA
4
A
ALA
5
15
3_554
A
ALA
4
A
ALA
5
15
1_555
A
SER
5
A
SER
6
15
1_555
A
BB9
6
A
BB9
7
15
1_555
A
THR
7
A
THR
8
15
1_555
A
TS9
10
A
TS9
11
15
1_555
A
BB9
11
A
BB9
12
15
6_465
A
THR
12
A
THR
13
15
1_555
A
BB9
13
A
BB9
14
15
1_555
A
NH2
18
A
NH2
19
15
6_455
A
HOH
2004
B
HOH
15
1_555
A
QUA
0
A
QUA
1
3
6_555
A
BB9
6
A
BB9
7
3
7_555
A
DHA
17
A
DHA
18
3
1_555
A
QUA
0
A
QUA
1
11
1_555
A
QUA
0
A
QUA
1
11
4_455
A
QUA
0
A
QUA
1
11
6_565
A
NH2
18
A
NH2
19
11
1_555
A
NH2
18
A
NH2
19
11
7_555
A
HOH
2001
B
HOH
11
8_665
A
HOH
2001
B
HOH
11
1_555
A
HOH
2002
B
HOH
11
8_665
A
HOH
2002
B
HOH
11
1_555
A
HOH
2003
B
HOH
11
1_555
A
HOH
2004
B
HOH
11
1_555
96
P 43 21 2