NPIDB: 5XYM structure

General information

PDB ID

5XYM

Title

LARGE SUBUNIT OF MYCOBACTERIUM SMEGMATIS

PDB header

RIBOSOME

Date

2017-07-09

Experimental method

ELECTRON MICROSCOPY

Resolution (A)

3.08

Kind

rna

Organism


Download complex	View in Jmol

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PDB	PDBe	MMDB	Jena	OCA
CATH	PDBsum	HSSP	PDBePISA	UniProt
ProteopediA	BIPA
	PRIDB

Composition of PDB entry and biounits
File:	Protein chains:	DNA chains:	RNA chains:	No. of models:	Action:

PDB entry:

pdb5xym.pdb	01234CDEFGHJKLMNOPQRSTUVWXYZa		AB	0

Biounits:

5xym.pdb1.pdb	01234CDEFGHJKLMNOPQRSTUVWXYZa		AB	1

Pfam domains
Name:	Type:	Domain:	E-value:	Significance:	Clan:	Prot. chain:	Start res.:	End res.:	Nuc. chains:	Int. mode:	Action:

Ribosomal_L36	Domain	A0QSL4_1-37	2e-18	1	No_clan	4	1	37	A
Ribosomal_L2_C	Domain	A0QSD4_126-251	5e-55	1	CL0107	C	126	251	A
Ribosomal_L2	Domain	A0QSD4_42-119	7.2e-34	1	CL0021	C	42	119	A
Ribosomal_L5_C	Domain	A0QSG1_91-184	8.6e-35	1	No_clan	F	91	184	AB
Ribosomal_L5	Domain	A0QSG1_31-87	9.5e-26	1	CL0652	F	31	87	AB
Ribosomal_L6	Domain	A0QSG4_91-166	4.9e-21	1	No_clan	G	91	166	A
Ribosomal_L6	Domain	A0QSG4_11-83	0.00033	0	No_clan	G	13	83	A
Ribosomal_L9_N	Domain	A0R7F6_1-39	2.9e-13	1	No_clan	H	1	39	A
Ribosomal_L14	Domain	A0QSF9_1-122	3.2e-55	1	No_clan	K	1	122	A
Ribosomal_L22	Domain	A0QSD6_12-115	8.2e-37	1	No_clan	S	12	115	A
Ribosomal_L25p	Domain	A0R3D2_11-97	1.8e-24	1	No_clan	V	11	97	B
Ribosomal_TL5_C	Domain	A0R3D2_105-185	7.3e-13	1	No_clan	V	97	183
Ribosomal_L30	Domain	A0QSG7_4-54	1.3e-18	1	No_clan	Z	4	54	A
Ribosomal_L32p	Family	A0R3I9_2-50	3.2e-14	1	CL0167	0	2	50	A
Ribosomal_L33	Family	A0R551_8-52	1.2e-11	1	CL0167	1	8	52	A
Ribosomal_L34	Family	A0R7K0_4-47	6e-19	1	No_clan	2	4	47	A
Ribosomal_L35p	Family	A0QYU7_2-62	1.1e-24	1	No_clan	3	2	62	A
Ribosomal_L3	Family	A0QSD1_80-191	2e-18	1	CL0575	D	79	191	A
Ribosomal_L4	Family	A0QSD2_18-206	1.3e-65	1	No_clan	E	18	206	A
Ribosomal_L13	Family	A0QSP8_13-131	1.9e-54	1	No_clan	J	14	138	A
Ribosomal_L27A	Family	A0QSG8_29-146	8.6e-32	1	CL0588	L	29	146	A
Ribosomal_L16	Family	A0QSD8_4-132	4.7e-44	1	No_clan	M	4	132	A
Ribosomal_L17	Family	A0QSL9_20-116	5.3e-38	1	No_clan	N	20	116	A
Ribosomal_L18p	Family	A0QSG5_12-127	2.4e-34	1	CL0267	O	12	127	A
Ribosomal_L19	Family	A0QV42_2-112	8.1e-51	1	CL0107	P	2	112	A
Ribosomal_L20	Family	A0QYU6_3-109	1.3e-41	1	No_clan	Q	3	109	A
Ribosomal_L21p	Family	A0R151_3-102	7.5e-34	1	No_clan	R	3	102	A
Ribosomal_L23	Family	A0QSD3_9-95	5e-31	1	No_clan	T	9	95	A
ribosomal_L24	Family	A0QSG0_38-105	2.2e-15	1	No_clan	U	36	105	A
KOW	Family	A0QSG0_5-36	1.8e-08	1	CL0107	U	5	36	A
Ribosomal_L27	Family	A0R150_8-80	2.9e-33	1	No_clan	W	8	80	AB
Ribosomal_L28	Family	A0QV03_3-61	1.6e-22	1	No_clan	X	3	61	A
Ribosomal_L29	Family	A0QSD9_8-64	2.7e-25	1	CL0346	Y	8	64	A

SCOP domains
No SCOP domains

GO terms
Protein chains:	GO type:	GO description:
0=1-57	C	large ribosomal subunit
0=1-57	F	structural constituent of ribosome
0=1-57	P	translation
1=1-54	C	ribosome
1=1-54	F	structural constituent of ribosome
1=1-54	P	translation
2=1-47	C	ribosome
2=1-47	F	structural constituent of ribosome
2=1-47	P	translation
3=1-64	C	ribosome
3=1-64	F	structural constituent of ribosome
3=1-64	P	translation
4=1-37	C	ribosome
4=1-37	F	structural constituent of ribosome
4=1-37	P	translation
C=1-278	C	large ribosomal subunit
C=1-278	F	rRNA binding
C=1-278	F	structural constituent of ribosome
C=1-278	F	transferase activity
C=1-278	P	translation
D=1-217	C	ribosome
D=1-217	F	rRNA binding
D=1-217	F	structural constituent of ribosome
D=1-217	P	translation
E=1-215	C	ribosome
E=1-215	F	rRNA binding
E=1-215	F	structural constituent of ribosome
E=1-215	P	translation
F=1-187	C	ribosome
F=1-187	F	rRNA binding
F=1-187	F	structural constituent of ribosome
F=1-187	F	tRNA binding
F=1-187	P	translation
G=1-179	C	ribosome
G=1-179	F	rRNA binding
G=1-179	F	structural constituent of ribosome
G=1-179	P	translation
H=1-151	C	ribosome
H=1-151	F	rRNA binding
H=1-151	F	structural constituent of ribosome
H=1-151	P	translation
J=1-147	C	ribosome
J=1-147	F	structural constituent of ribosome
J=1-147	P	translation
K=1-122	C	large ribosomal subunit
K=1-122	F	rRNA binding
K=1-122	F	structural constituent of ribosome
K=1-122	P	translation
M=1-138	C	ribosome
M=1-138	F	rRNA binding
M=1-138	F	structural constituent of ribosome
M=1-138	F	tRNA binding
M=1-138	P	translation
N=1-199	C	ribosome
N=1-199	F	structural constituent of ribosome
N=1-199	P	translation
P=1-113	C	ribosome
P=1-113	F	structural constituent of ribosome
P=1-113	P	translation
Q=1-129	C	ribosome
Q=1-129	F	rRNA binding
Q=1-129	F	structural constituent of ribosome
Q=1-129	P	ribosomal large subunit assembly
Q=1-129	P	translation
R=1-103	C	ribosome
R=1-103	F	rRNA binding
R=1-103	F	structural constituent of ribosome
R=1-103	P	translation
S=1-153	C	large ribosomal subunit
S=1-153	F	rRNA binding
S=1-153	F	structural constituent of ribosome
S=1-153	P	translation
T=1-100	C	ribosome
T=1-100	F	rRNA binding
T=1-100	F	structural constituent of ribosome
T=1-100	P	translation
U=1-105	C	ribosome
U=1-105	F	rRNA binding
U=1-105	F	structural constituent of ribosome
U=1-105	P	translation
W=1-88	C	ribosome
W=1-88	F	structural constituent of ribosome
W=1-88	P	translation
Y=1-77	C	ribosome
Y=1-77	F	structural constituent of ribosome
Y=1-77	P	translation
Z=1-61	C	large ribosomal subunit
Z=1-61	F	structural constituent of ribosome
Z=1-61	P	translation

Sequences

Download file with secondary structure created by Stride

5xym.pdb1.pdb: [ download sequences in FASTA format ]

0 (protein):