Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6LKQ

The Structural Basis for Inhibition of Ribosomal Translocation by Viomycin

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
0	0003735	molecular_function	structural constituent of ribosome
0	0005840	cellular_component	ribosome
0	0006412	biological_process	translation
1	0003735	molecular_function	structural constituent of ribosome
1	0005840	cellular_component	ribosome
1	0006412	biological_process	translation
1	0015934	cellular_component	large ribosomal subunit
2	0003723	molecular_function	RNA binding
2	0003735	molecular_function	structural constituent of ribosome
2	0005840	cellular_component	ribosome
2	0006412	biological_process	translation
2	0015934	cellular_component	large ribosomal subunit
2	0019843	molecular_function	rRNA binding
2	0022625	cellular_component	cytosolic large ribosomal subunit
2	1990904	cellular_component	ribonucleoprotein complex
3	0003735	molecular_function	structural constituent of ribosome
3	0005840	cellular_component	ribosome
3	0006412	biological_process	translation
3	0019843	molecular_function	rRNA binding
4	0003735	molecular_function	structural constituent of ribosome
4	0005840	cellular_component	ribosome
4	0006412	biological_process	translation
5	0003735	molecular_function	structural constituent of ribosome
5	0005840	cellular_component	ribosome
5	0006412	biological_process	translation
6	0003735	molecular_function	structural constituent of ribosome
6	0005840	cellular_component	ribosome
6	0006412	biological_process	translation
8	0003735	molecular_function	structural constituent of ribosome
8	0005840	cellular_component	ribosome
8	0006412	biological_process	translation
8	0019843	molecular_function	rRNA binding
9	0003723	molecular_function	RNA binding
9	0003735	molecular_function	structural constituent of ribosome
9	0005840	cellular_component	ribosome
9	0006412	biological_process	translation
A	0003735	molecular_function	structural constituent of ribosome
A	0005840	cellular_component	ribosome
A	0006412	biological_process	translation
A	0015935	cellular_component	small ribosomal subunit
A	0022627	cellular_component	cytosolic small ribosomal subunit
A	1990904	cellular_component	ribonucleoprotein complex
B	0003676	molecular_function	nucleic acid binding
B	0003723	molecular_function	RNA binding
B	0003735	molecular_function	structural constituent of ribosome
B	0006412	biological_process	translation
C	0003723	molecular_function	RNA binding
C	0003735	molecular_function	structural constituent of ribosome
C	0005840	cellular_component	ribosome
C	0006412	biological_process	translation
C	0015935	cellular_component	small ribosomal subunit
C	0019843	molecular_function	rRNA binding
C	0042274	biological_process	ribosomal small subunit biogenesis
C	1990904	cellular_component	ribonucleoprotein complex
D	0003723	molecular_function	RNA binding
D	0003735	molecular_function	structural constituent of ribosome
D	0005840	cellular_component	ribosome
D	0006412	biological_process	translation
D	0015935	cellular_component	small ribosomal subunit
E	0003735	molecular_function	structural constituent of ribosome
E	0005840	cellular_component	ribosome
E	0006412	biological_process	translation
E	0019843	molecular_function	rRNA binding
F	0003723	molecular_function	RNA binding
F	0003735	molecular_function	structural constituent of ribosome
F	0006412	biological_process	translation
F	0015935	cellular_component	small ribosomal subunit
G	0003735	molecular_function	structural constituent of ribosome
G	0005840	cellular_component	ribosome
G	0006412	biological_process	translation
H	0003735	molecular_function	structural constituent of ribosome
H	0005840	cellular_component	ribosome
H	0006412	biological_process	translation
I	0003723	molecular_function	RNA binding
I	0003735	molecular_function	structural constituent of ribosome
I	0005840	cellular_component	ribosome
I	0006412	biological_process	translation
J	0003735	molecular_function	structural constituent of ribosome
J	0005840	cellular_component	ribosome
J	0006412	biological_process	translation
K	0003735	molecular_function	structural constituent of ribosome
K	0005840	cellular_component	ribosome
K	0006412	biological_process	translation
K	0015935	cellular_component	small ribosomal subunit
L	0003676	molecular_function	nucleic acid binding
L	0003723	molecular_function	RNA binding
L	0003735	molecular_function	structural constituent of ribosome
L	0005840	cellular_component	ribosome
L	0006412	biological_process	translation
M	0003723	molecular_function	RNA binding
M	0003735	molecular_function	structural constituent of ribosome
M	0005737	cellular_component	cytoplasm
M	0005840	cellular_component	ribosome
M	0006412	biological_process	translation
M	0015935	cellular_component	small ribosomal subunit
M	0019843	molecular_function	rRNA binding
M	1990904	cellular_component	ribonucleoprotein complex
N	0003735	molecular_function	structural constituent of ribosome
N	0005840	cellular_component	ribosome
N	0006412	biological_process	translation
O	0003735	molecular_function	structural constituent of ribosome
O	0005840	cellular_component	ribosome
O	0006412	biological_process	translation
P	0003735	molecular_function	structural constituent of ribosome
P	0005840	cellular_component	ribosome
P	0006412	biological_process	translation
Q	0003735	molecular_function	structural constituent of ribosome
Q	0005840	cellular_component	ribosome
Q	0006412	biological_process	translation
R	0003723	molecular_function	RNA binding
R	0003735	molecular_function	structural constituent of ribosome
R	0005840	cellular_component	ribosome
R	0006412	biological_process	translation
R	0015935	cellular_component	small ribosomal subunit
S	0003723	molecular_function	RNA binding
S	0003735	molecular_function	structural constituent of ribosome
S	0005840	cellular_component	ribosome
S	0006412	biological_process	translation
T	0003735	molecular_function	structural constituent of ribosome
T	0005840	cellular_component	ribosome
T	0006412	biological_process	translation
U	0003723	molecular_function	RNA binding
U	0003735	molecular_function	structural constituent of ribosome
U	0005840	cellular_component	ribosome
U	0006412	biological_process	translation
U	0015934	cellular_component	large ribosomal subunit
U	0016740	molecular_function	transferase activity
V	0003735	molecular_function	structural constituent of ribosome
V	0005840	cellular_component	ribosome
V	0006412	biological_process	translation
W	0003735	molecular_function	structural constituent of ribosome
W	0005840	cellular_component	ribosome
W	0006412	biological_process	translation
X	0003735	molecular_function	structural constituent of ribosome
X	0005840	cellular_component	ribosome
X	0006412	biological_process	translation
Y	0003735	molecular_function	structural constituent of ribosome
Y	0005840	cellular_component	ribosome
Y	0006412	biological_process	translation
Y	0019843	molecular_function	rRNA binding
Z	0003735	molecular_function	structural constituent of ribosome
Z	0005840	cellular_component	ribosome
Z	0006412	biological_process	translation
a	0003735	molecular_function	structural constituent of ribosome
a	0005840	cellular_component	ribosome
a	0006412	biological_process	translation
a	0015934	cellular_component	large ribosomal subunit
b	0003735	molecular_function	structural constituent of ribosome
b	0005840	cellular_component	ribosome
b	0006412	biological_process	translation
c	0003723	molecular_function	RNA binding
c	0003735	molecular_function	structural constituent of ribosome
c	0005840	cellular_component	ribosome
c	0006412	biological_process	translation
d	0003735	molecular_function	structural constituent of ribosome
d	0005840	cellular_component	ribosome
d	0006412	biological_process	translation
d	0008097	molecular_function	5S rRNA binding
e	0003735	molecular_function	structural constituent of ribosome
e	0005840	cellular_component	ribosome
e	0006412	biological_process	translation
f	0003735	molecular_function	structural constituent of ribosome
f	0005840	cellular_component	ribosome
f	0006412	biological_process	translation
g	0003735	molecular_function	structural constituent of ribosome
g	0005840	cellular_component	ribosome
g	0006412	biological_process	translation
h	0003735	molecular_function	structural constituent of ribosome
h	0006412	biological_process	translation
h	0015934	cellular_component	large ribosomal subunit
i	0003735	molecular_function	structural constituent of ribosome
i	0006412	biological_process	translation
i	0015934	cellular_component	large ribosomal subunit
j	0003735	molecular_function	structural constituent of ribosome
j	0005840	cellular_component	ribosome
j	0006412	biological_process	translation
k	0003735	molecular_function	structural constituent of ribosome
k	0005840	cellular_component	ribosome
k	0006412	biological_process	translation
l	0003735	molecular_function	structural constituent of ribosome
l	0005840	cellular_component	ribosome
l	0006412	biological_process	translation
m	0003735	molecular_function	structural constituent of ribosome
m	0005840	cellular_component	ribosome
m	0006412	biological_process	translation
n	0003735	molecular_function	structural constituent of ribosome
n	0006412	biological_process	translation
n	0015934	cellular_component	large ribosomal subunit
o	0003735	molecular_function	structural constituent of ribosome
o	0005840	cellular_component	ribosome
o	0006412	biological_process	translation
p	0003735	molecular_function	structural constituent of ribosome
p	0005840	cellular_component	ribosome
p	0006412	biological_process	translation
q	0003735	molecular_function	structural constituent of ribosome
q	0005840	cellular_component	ribosome
q	0006412	biological_process	translation
r	0003735	molecular_function	structural constituent of ribosome
r	0005840	cellular_component	ribosome
r	0006412	biological_process	translation
v	0000166	molecular_function	nucleotide binding
v	0003747	molecular_function	translation release factor activity
v	0003924	molecular_function	GTPase activity
v	0005525	molecular_function	GTP binding
v	0005737	cellular_component	cytoplasm
v	0005829	cellular_component	cytosol
v	0006412	biological_process	translation
v	0006415	biological_process	translational termination
v	0006449	biological_process	regulation of translational termination
v	0016149	molecular_function	translation release factor activity, codon specific
v	0016150	molecular_function	translation release factor activity, codon nonspecific
v	0097216	molecular_function	guanosine tetraphosphate binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	binding site for Ligand residues UAL AA 5 through SER AA 3 bound to SER AA 4

Chain	Residue
7	KBE1
t	C1934
t	A1960
t	C1961
t	C1962
AA	SER4
BA	5OH6
s	G1416
s	C1484
s	U1485
s	G1486
t	A1932
t	G1933

site_id	AC2
Number of Residues	8
Details	binding site for Ligand residues UAL BA 5 through SER BA 3 bound to SER BA 4

Chain	Residue
7	KBE1
AA	5OH6
BA	SER4
t	U1917
t	A1918
t	G1930
t	C1962
t	U1963

site_id	AC3
Number of Residues	9
Details	binding site for Viomycin chain y

Chain	Residue
K	THR40
s	A1408
s	G1491
s	A1492
s	A1493
s	G1494
s	U1495
s	C1496
t	C1914

site_id	AC4
Number of Residues	13
Details	binding site for Viomycin chain z

Chain	Residue
K	LYS42
K	LYS43
s	U13
s	U14
s	A16
s	C526
s	G527
s	C912
s	A913
s	A914
s	A915
s	U1490
s	G1491

site_id	AC5
Number of Residues	13
Details	binding site for Viomycin chain 7

Chain	Residue
AA	SER4
AA	UAL5
BA	KBE1
BA	DPP2
s	U793
s	G1517
t	A1919
t	C1920
t	U1931
t	A1932
t	G1933
t	C1967
t	G1968

site_id	AC6
Number of Residues	14
Details	binding site for Viomycin chain BA

Chain	Residue
B	ASN7
B	GLY8
B	ILE9
B	ARG10
B	LEU174
B	TYR183
M	MET88
s	U1060
s	G1061
s	U1189
s	G1190
s	A1191
s	C1192
s	G1193

Functional Information from PROSITE/UniProt

site_id	PS00049
Number of Residues	27
Details	RIBOSOMAL_L14 Ribosomal protein L14 signature. AVVVrtkkgvrrp.DGsvirFdgNacVL

Chain	Residue	Details
1	ALA60-LEU86

site_id	PS00052
Number of Residues	27
Details	RIBOSOMAL_S7 Ribosomal protein S7 signature. SeLlakFVnilmvdGKKstaesIVysA

Chain	Residue	Details
F	SER19-ALA45

site_id	PS00053
Number of Residues	18
Details	RIBOSOMAL_S8 Ribosomal protein S8 signature. GiaVVSTSkGVMtdraAR

Chain	Residue	Details
G	GLY99-ARG116

site_id	PS00054
Number of Residues	23
Details	RIBOSOMAL_S11 Ribosomal protein S11 signature. IrALnaA.GFrItnitDvTPiPHN

Chain	Residue	Details
J	ILE96-ASN118

site_id	PS00055
Number of Residues	8
Details	RIBOSOMAL_S12 Ribosomal protein S12 signature. KkPNSAlR

Chain	Residue	Details
K	LYS42-ARG49

site_id	PS00056
Number of Residues	13
Details	RIBOSOMAL_S17 Ribosomal protein S17 signature. GDvVeIrEcRPLS

Chain	Residue	Details
P	GLY55-SER67

site_id	PS00057
Number of Residues	24
Details	RIBOSOMAL_S18 Ribosomal protein S18 signature. IDYkd.IatLknYITEs.GKIvpsRI

Chain	Residue	Details
Q	ILE20-ILE43

site_id	PS00061
Number of Residues	29
Details	ADH_SHORT Short-chain dehydrogenases/reductases family signature. PdhkhavialTsiYGVGKTRSkAILaAAG

Chain	Residue	Details
L	PRO9-GLY37

site_id	PS00301
Number of Residues	16
Details	G_TR_1 Translational (tr)-type guanine nucleotide-binding (G) domain signature. DWmemEKqRGISIttS

Chain	Residue	Details
v	ASP58-SER73

site_id	PS00323
Number of Residues	25
Details	RIBOSOMAL_S19 Ribosomal protein S19 signature. NGRqhvpvfVtdemVGhkLGEFapT

Chain	Residue	Details
R	ASN52-THR76

site_id	PS00358
Number of Residues	17
Details	RIBOSOMAL_L5 Ribosomal protein L5 signature. LaaISGQkpLiTkARkS

Chain	Residue	Details
X	LEU56-SER72

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

Chain	Residue	Details
Z	ARG126-ASP141

site_id	PS00360
Number of Residues	19
Details	RIBOSOMAL_S9 Ribosomal protein S9 signature. GGGisGQagAirhGiTRAL

Chain	Residue	Details
H	GLY68-LEU86

site_id	PS00361
Number of Residues	16
Details	RIBOSOMAL_S10 Ribosomal protein S10 signature. AkrtGAqvrGPIpLPT

Chain	Residue	Details
I	ALA29-THR44

site_id	PS00362
Number of Residues	31
Details	RIBOSOMAL_S15 Ribosomal protein S15 signature. LqgHFaehKkDhhSrrgLlrMvsqrrkLldY

Chain	Residue	Details
N	LEU38-TYR68

site_id	PS00430
Number of Residues	66
Details	TONB_DEPENDENT_REC_1 TonB-dependent receptor (TBDR) proteins signature 1. mireerllkvlraphvsekastameksntivlkvakdatkaeikaavqklfevevevv.........................................................NTLVVKGK

Chain	Residue	Details
b	MET1-LYS66

site_id	PS00464
Number of Residues	25
Details	RIBOSOMAL_L22 Ribosomal protein L22 signature. KriMpRAkGRadrilkrtSHITVvV

Chain	Residue	Details
a	LYS83-VAL107

site_id	PS00467
Number of Residues	12
Details	RIBOSOMAL_L2 Ribosomal protein L2 signature. PtvRGTAmNPvD

Chain	Residue	Details
U	PRO217-ASP228

site_id	PS00474
Number of Residues	24
Details	RIBOSOMAL_L3 Ribosomal protein L3 signature. FadvkkvDvtGtSkGKGfaGtvkR

Chain	Residue	Details
V	PHE101-ARG124

site_id	PS00475
Number of Residues	31
Details	RIBOSOMAL_L15 Ribosomal protein L15 signature. KVILaGeVttp..VtVrglrVTkgAraaIeaaG

Chain	Residue	Details
2	LYS109-GLY139

site_id	PS00525
Number of Residues	9
Details	RIBOSOMAL_L6_1 Ribosomal protein L6 signature 1. PEpYKGKGV

Chain	Residue	Details
Y	PRO153-VAL161

site_id	PS00527
Number of Residues	23
Details	RIBOSOMAL_S14 Ribosomal protein S14 signature. R.CrqtgrphgflrkFGLSRiKVR

Chain	Residue	Details
M	ARG62-ARG84

site_id	PS00548
Number of Residues	35
Details	RIBOSOMAL_S3 Ribosomal protein S3 signature. ARtewyreGrVplHt..LradIDyntseahTtyGviG

Chain	Residue	Details
B	ALA162-GLY196

site_id	PS00579
Number of Residues	15
Details	RIBOSOMAL_L29 Ribosomal protein L29 signature. QSHLLKqVRRDVARV

Chain	Residue	Details
g	GLN39-VAL53

site_id	PS00582
Number of Residues	20
Details	RIBOSOMAL_L33 Ribosomal protein L33 signature. YtTtKNkrtkPekLElkKFD

Chain	Residue	Details
j	TYR20-ASP39

site_id	PS00585
Number of Residues	33
Details	RIBOSOMAL_S5 Ribosomal protein S5 signature. GRifsFtAltVVGDgn.GrVGfGygkar.EVpa.AI

Chain	Residue	Details
D	GLY27-ILE59

site_id	PS00586
Number of Residues	12
Details	RIBOSOMAL_L16_1 Ribosomal protein L16 signature 1. KRqGKIWIRVFP

Chain	Residue	Details
3	LYS58-PRO69

site_id	PS00632
Number of Residues	25
Details	RIBOSOMAL_S4 Ribosomal protein S4 signature. LEgRLdnvVYRmgfGaTraeARqLV

Chain	Residue	Details
C	LEU93-VAL117

site_id	PS00634
Number of Residues	33
Details	RIBOSOMAL_L30 Ribosomal protein L30 signature. TLlgLgLrRigHtVeredtpairgMInaVsfMV

Chain	Residue	Details
h	THR22-VAL54

site_id	PS00646
Number of Residues	14
Details	RIBOSOMAL_S13_1 Ribosomal protein S13 signature. RGlRHrrGlpVRGQ

Chain	Residue	Details
L	ARG86-GLN99

site_id	PS00701
Number of Residues	12
Details	RIBOSOMAL_L16_2 Ribosomal protein L16 signature 2. RMGkGKGnveyW

Chain	Residue	Details
3	ARG81-TRP92

site_id	PS00732
Number of Residues	10
Details	RIBOSOMAL_S16 Ribosomal protein S16 signature. VtIRLARHGA

Chain	Residue	Details
O	VAL2-ALA11

site_id	PS00783
Number of Residues	23
Details	RIBOSOMAL_L13 Ribosomal protein L13 signature. VKGMLPkgpl.GRamfrkLkVYaG

Chain	Residue	Details
0	VAL105-GLY127

site_id	PS00784
Number of Residues	20
Details	RIBOSOMAL_L34 Ribosomal protein L34 signature. KRTFQpsvlkRnrsh.GFraR

Chain	Residue	Details
k	LYS2-ARG21

site_id	PS00828
Number of Residues	27
Details	RIBOSOMAL_L36 Ribosomal protein L36 signature. CrnCkiVkRdgvIrViCsaepKHkQrQ

Chain	Residue	Details
m	CYS11-GLN37

site_id	PS00831
Number of Residues	15
Details	RIBOSOMAL_L27 Ribosomal protein L27 signature. GsIIvRQRGtkfhaG

Chain	Residue	Details
e	GLY33-GLY47

site_id	PS00936
Number of Residues	27
Details	RIBOSOMAL_L35 Ribosomal protein L35 signature. KTVrGAaKRFkktgkggfkhkhanl.RH

Chain	Residue	Details
l	LYS4-HIS30

site_id	PS00937
Number of Residues	17
Details	RIBOSOMAL_L20 Ribosomal protein L20 signature. KrqfRqLWIARINaaaR

Chain	Residue	Details
8	LYS53-ARG69

site_id	PS00963
Number of Residues	25
Details	RIBOSOMAL_S2_2 Ribosomal protein S2 signature 2. PdaLFViDadhEhiaIkEannlGIP

Chain	Residue	Details
A	PRO157-PRO181

site_id	PS01015
Number of Residues	16
Details	RIBOSOMAL_L19 Ribosomal protein L19 signature. VkRrGAVR.KAKLYYLR

Chain	Residue	Details
6	VAL85-ARG100

site_id	PS01048
Number of Residues	10
Details	RIBOSOMAL_S6 Ribosomal protein S6 signature. GrRQLAYpIN

Chain	Residue	Details
E	GLY43-ASN52

site_id	PS01108
Number of Residues	18
Details	RIBOSOMAL_L24 Ribosomal protein L24 signature. DDeViVLtGkdKGkr.GkV

Chain	Residue	Details
c	ASP7-VAL24

site_id	PS01109
Number of Residues	35
Details	RIBOSOMAL_L10 Ribosomal protein L10 signature. KqaIvaeVSevakgalsaVvaDsrGVTVdKMteLR

Chain	Residue	Details
n	LYS8-ARG42

site_id	PS01167
Number of Residues	23
Details	RIBOSOMAL_L17 Ribosomal protein L17 signature. IkTTlpKaKelrrvvEpLITlAK

Chain	Residue	Details
4	ILE34-LYS56

site_id	PS01169
Number of Residues	23
Details	RIBOSOMAL_L21 Ribosomal protein L21 signature. VkivKfrrRKhyrkqqGHRQwfT

Chain	Residue	Details
9	VAL72-THR94

site_id	PS01181
Number of Residues	13
Details	RIBOSOMAL_S21 Ribosomal protein S21 signature. DvALRRFKRsceK

Chain	Residue	Details
T	ASP12-LYS24

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)