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5D8H
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (95 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON
Authors
:
A. G. Gabdulkhakov, I. V. Mitroshin, M. B. Garber
Date
:
17 Aug 15 (Deposition) - 24 Aug 16 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Ribosome, P-Stalk, Archaea, Antibiotic, Thiostrepton, Ribosomal Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. G. Gabdulkhakov, I. V. Mitroshin, M. B. Garber
Crystal Structure Of The Base Of The Ribosomal P Stalk From Methanococcus Jannaschii With Antibiotic Thiostrepton
To Be Published
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close entry info
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Hetero Components
(12, 42)
Info
All Hetero Components
01a: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9a)
01b: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9b)
01c: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9c)
01d: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9d)
02a: (2Z)-2-AMINOBUT-2-ENOIC ACID (DBUa)
03a: D-CYSTEINE (DCYa)
04a: 2-AMINO-ACRYLIC ACID (DHAa)
04b: 2-AMINO-ACRYLIC ACID (DHAb)
04c: 2-AMINO-ACRYLIC ACID (DHAc)
05a: MAGNESIUM ION (MGa)
05b: MAGNESIUM ION (MGb)
05c: MAGNESIUM ION (MGc)
05d: MAGNESIUM ION (MGd)
05e: MAGNESIUM ION (MGe)
05f: MAGNESIUM ION (MGf)
05g: MAGNESIUM ION (MGg)
05h: MAGNESIUM ION (MGh)
05i: MAGNESIUM ION (MGi)
05j: MAGNESIUM ION (MGj)
05k: MAGNESIUM ION (MGk)
06a: 3-HYDROXY-2-IMINOPROPANOIC ACID (MH6a)
07a: SELENOMETHIONINE (MSEa)
07b: SELENOMETHIONINE (MSEb)
07c: SELENOMETHIONINE (MSEc)
07d: SELENOMETHIONINE (MSEd)
07e: SELENOMETHIONINE (MSEe)
07f: SELENOMETHIONINE (MSEf)
07g: SELENOMETHIONINE (MSEg)
07h: SELENOMETHIONINE (MSEh)
07i: SELENOMETHIONINE (MSEi)
07j: SELENOMETHIONINE (MSEj)
07k: SELENOMETHIONINE (MSEk)
08a: SODIUM ION (NAa)
08b: SODIUM ION (NAb)
08c: SODIUM ION (NAc)
08d: SODIUM ION (NAd)
09a: AMINO GROUP (NH2a)
10a: 8-HYDROXY-4-(1-HYDROXYETHYL)QUINOL... (QUAa)
11a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
11b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
11c: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSc)
12a: (2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3... (TS9a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BB9
4
Mod. Amino Acid
(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
2
DBU
1
Mod. Amino Acid
(2Z)-2-AMINOBUT-2-ENOIC ACID
3
DCY
1
Mod. Amino Acid
D-CYSTEINE
4
DHA
3
Mod. Amino Acid
2-AMINO-ACRYLIC ACID
5
MG
11
Ligand/Ion
MAGNESIUM ION
6
MH6
1
Mod. Amino Acid
3-HYDROXY-2-IMINOPROPANOIC ACID
7
MSE
11
Mod. Amino Acid
SELENOMETHIONINE
8
NA
4
Ligand/Ion
SODIUM ION
9
NH2
1
Mod. Amino Acid
AMINO GROUP
10
QUA
1
Mod. Amino Acid
8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC ACID
11
TRS
3
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
12
TS9
1
Mod. Amino Acid
(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC ACID
[
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Sites
(25, 25)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G A:1166 , HOH A:1405 , HOH A:1414 , HOH A:1417 , HOH A:1429 , HOH A:1434
binding site for residue MG A 1301
02
AC2
SOFTWARE
A A:1183 , G A:1203 , U A:1204 , HOH A:1409 , HOH A:1416 , HOH A:1422 , HOH A:1428
binding site for residue MG A 1302
03
AC3
SOFTWARE
G A:1173 , A A:1180 , C A:1182 , G A:1184 , NA A:1313 , HOH A:1432 , HOH A:1437
binding site for residue MG A 1303
04
AC4
SOFTWARE
HOH A:1403 , HOH A:1420 , HOH A:1431 , HOH A:1440 , HOH A:1442 , HOH A:1454
binding site for residue MG A 1304
05
AC5
SOFTWARE
HOH A:1413 , HOH A:1424 , HOH A:1425 , HOH A:1439 , HOH A:1448 , HOH A:1451
binding site for residue MG A 1305
06
AC6
SOFTWARE
HOH A:1412 , HOH A:1436 , HOH A:1445 , HOH A:1446 , HOH A:1449 , HOH A:1453
binding site for residue MG A 1306
07
AC7
SOFTWARE
G A:1181 , A A:1208 , HOH A:1408 , HOH A:1427 , HOH A:1435 , HOH A:1457
binding site for residue MG A 1307
08
AC8
SOFTWARE
U A:1175 , HOH A:1421 , HOH A:1438 , HOH A:1441 , HOH A:1444
binding site for residue MG A 1308
09
AC9
SOFTWARE
G A:1157 , G A:1220 , HOH A:1415 , HOH A:1426 , HOH A:1452 , HOH A:1456
binding site for residue MG A 1309
10
AD1
SOFTWARE
G A:1223 , HOH A:1402 , HOH A:1430 , HOH A:1443 , HOH A:1450 , HOH A:1455 , HOH A:1458
binding site for residue MG A 1310
11
AD2
SOFTWARE
U A:1176 , A A:1177 , HOH A:1447
binding site for residue NA A 1311
12
AD3
SOFTWARE
G A:1169 , U A:1171
binding site for residue NA A 1312
13
AD4
SOFTWARE
A A:1179 , A A:1180 , C A:1182 , A A:1183 , MG A:1303 , HOH A:1401
binding site for residue NA A 1313
14
AD5
SOFTWARE
G A:1166 , A A:1167 , C A:1210
binding site for residue TRS A 1314
15
AD6
SOFTWARE
A A:1167 , G A:1168 , G A:1197 , G A:1199
binding site for residue TRS A 1315
16
AD7
SOFTWARE
ASP B:34 , MSE B:36
binding site for residue NA B 301
17
AD8
SOFTWARE
GLU B:82 , ASN B:85 , TYR B:86
binding site for residue TRS B 302
18
AD9
SOFTWARE
LYS C:110 , MSE C:113 , SER C:115 , HOH C:301 , HOH C:303
binding site for residue MG C 201
19
AE1
SOFTWARE
QUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12
binding site for Ligand residues BB9 D 13 through NH2 D 18 bound to SER D 5
20
AE2
SOFTWARE
A A:1177 , G A:1178 , A A:1205 , QUA D:0 , ALA D:4 , SER D:5 , DBU D:8 , DCY D:9 , THR D:12 , BB9 D:13
binding site for Ligand residues BB9 D 6 through THR D 7 bound to SER D 5
21
AE3
SOFTWARE
A A:1177 , A A:1205 , QUA D:0 , ALA D:4 , SER D:5 , THR D:7 , BB9 D:13
binding site for Ligand BB9 D 6 bound to SER D 5
22
AE4
SOFTWARE
ALA D:4 , SER D:5 , BB9 D:13 , BB9 D:15
binding site for Ligand MH6 D 14 bound to SER D 5
23
AE5
SOFTWARE
A A:1177 , G A:1178 , LYS B:25 , GLU B:74 , PRO C:18 , QUA D:0 , THR D:7 , THR D:12
binding site for Ligand residues DBU D 8 through BB9 D 11 bound to THR D 7
24
AE6
SOFTWARE
QUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12 , MH6 D:14
binding site for Ligand BB9 D 13 bound to THR D 12
25
AE7
SOFTWARE
QUA D:0 , ALA D:4 , SER D:5 , BB9 D:6 , THR D:7 , THR D:12 , MH6 D:14
binding site for Ligand BB9 D 13 bound to THR D 12
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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