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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5D8H

CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII WITH ANTIBIOTIC THIOSTREPTON

Functional Information from GO Data

Chain	GOid	namespace	contents
C	0003735	molecular_function	structural constituent of ribosome
C	0005840	cellular_component	ribosome
C	0006412	biological_process	translation
C	0015934	cellular_component	large ribosomal subunit
C	0019843	molecular_function	rRNA binding
C	0070180	molecular_function	large ribosomal subunit rRNA binding
C	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue MG A 1301

Chain	Residue
A	G1166
A	HOH1405
A	HOH1414
A	HOH1417
A	HOH1429
A	HOH1434

site_id	AC2
Number of Residues	7
Details	binding site for residue MG A 1302

Chain	Residue
A	HOH1409
A	HOH1416
A	HOH1422
A	HOH1428
A	A1183
A	G1203
A	U1204

site_id	AC3
Number of Residues	7
Details	binding site for residue MG A 1303

Chain	Residue
A	G1173
A	A1180
A	C1182
A	G1184
A	NA1313
A	HOH1432
A	HOH1437

site_id	AC4
Number of Residues	6
Details	binding site for residue MG A 1304

Chain	Residue
A	HOH1403
A	HOH1420
A	HOH1431
A	HOH1440
A	HOH1442
A	HOH1454

site_id	AC5
Number of Residues	6
Details	binding site for residue MG A 1305

Chain	Residue
A	HOH1413
A	HOH1424
A	HOH1425
A	HOH1439
A	HOH1448
A	HOH1451

site_id	AC6
Number of Residues	6
Details	binding site for residue MG A 1306

Chain	Residue
A	HOH1412
A	HOH1436
A	HOH1445
A	HOH1446
A	HOH1449
A	HOH1453

site_id	AC7
Number of Residues	6
Details	binding site for residue MG A 1307

Chain	Residue
A	G1181
A	A1208
A	HOH1408
A	HOH1427
A	HOH1435
A	HOH1457

site_id	AC8
Number of Residues	5
Details	binding site for residue MG A 1308

Chain	Residue
A	U1175
A	HOH1421
A	HOH1438
A	HOH1441
A	HOH1444

site_id	AC9
Number of Residues	6
Details	binding site for residue MG A 1309

Chain	Residue
A	G1157
A	G1220
A	HOH1415
A	HOH1426
A	HOH1452
A	HOH1456

site_id	AD1
Number of Residues	7
Details	binding site for residue MG A 1310

Chain	Residue
A	G1223
A	HOH1402
A	HOH1430
A	HOH1443
A	HOH1450
A	HOH1455
A	HOH1458

site_id	AD2
Number of Residues	3
Details	binding site for residue NA A 1311

Chain	Residue
A	U1176
A	A1177
A	HOH1447

site_id	AD3
Number of Residues	2
Details	binding site for residue NA A 1312

Chain	Residue
A	G1169
A	U1171

site_id	AD4
Number of Residues	6
Details	binding site for residue NA A 1313

Chain	Residue
A	A1179
A	A1180
A	C1182
A	A1183
A	MG1303
A	HOH1401

site_id	AD5
Number of Residues	3
Details	binding site for residue TRS A 1314

Chain	Residue
A	G1166
A	A1167
A	C1210

site_id	AD6
Number of Residues	4
Details	binding site for residue TRS A 1315

Chain	Residue
A	A1167
A	G1168
A	G1197
A	G1199

site_id	AD7
Number of Residues	2
Details	binding site for residue NA B 301

Chain	Residue
B	ASP34
B	MSE36

site_id	AD8
Number of Residues	4
Details	binding site for residue TRS B 302

Chain	Residue
B	GLU82
B	ASN85
B	ASN85
B	TYR86

site_id	AD9
Number of Residues	5
Details	binding site for residue MG C 201

Chain	Residue
C	LYS110
C	MSE113
C	SER115
C	HOH301
C	HOH303

site_id	AE1
Number of Residues	6
Details	binding site for Ligand residues BB9 D 13 through NH2 D 18 bound to SER D 5

Chain	Residue
D	QUA0
D	ALA4
D	SER5
D	BB96
D	THR7
D	THR12

site_id	AE2
Number of Residues	10
Details	binding site for Ligand residues BB9 D 6 through THR D 7 bound to SER D 5

Chain	Residue
A	A1205
D	QUA0
D	ALA4
D	SER5
D	DBU8
D	DCY9
D	THR12
D	BB913
A	A1177
A	G1178

site_id	AE3
Number of Residues	7
Details	binding site for Ligand BB9 D 6 bound to SER D 5

Chain	Residue
A	A1177
A	A1205
D	QUA0
D	ALA4
D	SER5
D	THR7
D	BB913

site_id	AE4
Number of Residues	4
Details	binding site for Ligand MH6 D 14 bound to SER D 5

Chain	Residue
D	ALA4
D	SER5
D	BB913
D	BB915

site_id	AE5
Number of Residues	8
Details	binding site for Ligand residues DBU D 8 through BB9 D 11 bound to THR D 7

Chain	Residue
A	A1177
A	G1178
B	LYS25
B	GLU74
C	PRO18
D	QUA0
D	THR7
D	THR12

site_id	AE6
Number of Residues	7
Details	binding site for Ligand BB9 D 13 bound to THR D 12

Chain	Residue
D	QUA0
D	ALA4
D	SER5
D	BB96
D	THR7
D	THR12
D	MH614

site_id	AE7
Number of Residues	7
Details	binding site for Ligand BB9 D 13 bound to THR D 12

Chain	Residue
D	QUA0
D	ALA4
D	SER5
D	BB96
D	THR7
D	THR12
D	MH614

Functional Information from PROSITE/UniProt

site_id	PS00359
Number of Residues	16
Details	RIBOSOMAL_L11 Ribosomal protein L11 signature. KeVlGTcgSMGvTVeG

Chain	Residue	Details
C	LYS123-GLY138

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: 2,3-didehydroalanine (Ser) => ECO:0000269\|PubMed:6885635

Chain	Residue	Details
D	DHA3
D	DHA16

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: (Z)-2,3-didehydrobutyrine => ECO:0000269\|PubMed:6885635

Chain	Residue	Details
D	DBU8

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: (3S,4R)-3,4-dihydroxyisoleucine => ECO:0000269\|PubMed:19338336

Chain	Residue	Details
D	TS910

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Serine amide => ECO:0000269\|PubMed:6885635

Chain	Residue	Details
D	DHA17

site_id	SWS_FT_FI5
Number of Residues	1
Details	CROSSLNK: 4-(1-hydroxyethyl)-7-isoleucino-2-(threonin-O3-ylcarbonyl)-7,8-dihydroquinolin-8-ol (Ile-Thr)

Chain	Residue	Details
D	ILE1

site_id	SWS_FT_FI6
Number of Residues	2
Details	CROSSLNK: Thiazole-4-carboxylic acid (Thr-Cys)

Chain	Residue	Details
D	THR12
D	BB913

site_id	SWS_FT_FI7
Number of Residues	4
Details	CROSSLNK: Thiazole-4-carboxylic acid (Ser-Cys)

Chain	Residue	Details
D	SER5
D	MH614
D	BB96
D	BB915

site_id	SWS_FT_FI8
Number of Residues	2
Details	CROSSLNK: (4S)-thiazoline-4-carboxylic acid (Thr-Cys)

Chain	Residue	Details
D	DBU8
D	DCY9

site_id	SWS_FT_FI9
Number of Residues	2
Details	CROSSLNK: Thiazole-4-carboxylic acid (Ile-Cys)

Chain	Residue	Details
D	TS910
D	BB911

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PDB entries from 2024-07-24

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