Het-PDB Navi2 (PDB: 4V9L)

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Data format:

Color scheme of protein:

Ligands
Code	Name	Link
FUA	Fusidic acid	PoSSuM
GDP	Guanosine-5'-diphosphate	PoSSuM
MG	Magnesium ion	PoSSuM

Non-standard Residues
Code	Name	Show
KBE	Beta-lysine
DPP	Diaminopropanoic acid
UAL	(2z)-2-amino-3-(carbamoylamino)prop-2-enoic acid
5OH	(2s)-amino[(4r,6s)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 4V9L

Code :

4V9L PDBj RCSB PDB PDBe

Header :

RIBOSOME/ANTIBIOTIC

Title :

70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC ACID/GDP, mRNA, and tRNA bound in the pe*/E state.

Release Data :

2014-07-09

Compound :

mol_id	molecule	chains
1	30S ribosomal protein S2	AB,CB

mol_id	molecule	chains
2	30S ribosomal protein S3	AC,CC

mol_id	molecule	chains
3	30S ribosomal protein S4	AD,CD

mol_id	molecule	chains
4	30S ribosomal protein S5	AE,CE

mol_id	molecule	chains
5	30S ribosomal protein S6	AF,CF

mol_id	molecule	chains
6	30S ribosomal protein S7	AG,CG

mol_id	molecule	chains
7	30S ribosomal protein S8	AH,CH

mol_id	molecule	chains
8	30S ribosomal protein S9	AI,CI

mol_id	molecule	chains
9	30S ribosomal protein S10	AJ,CJ

mol_id	molecule	chains
10	30S ribosomal protein S11	AK,CK

mol_id	molecule	chains
11	30S ribosomal protein S12	AL,CL

mol_id	molecule	chains
12	30S ribosomal protein S13	AM,CM

mol_id	molecule	chains
13	30S ribosomal protein S14 type Z	AN,CN

mol_id	molecule	chains
14	30S ribosomal protein S15	AO,CO

mol_id	molecule	chains
15	30S ribosomal protein S16	AP,CP

mol_id	molecule	chains
16	30S ribosomal protein S17	AQ,CQ

mol_id	molecule	chains
17	30S ribosomal protein S18	AR,CR

mol_id	molecule	chains
18	30S ribosomal protein S19	AS,CS

mol_id	molecule	chains
19	30S ribosomal protein S20	AT,CT

mol_id	molecule	chains
20	ribosomal RNA 16S	AA,CA

mol_id	molecule	chains
21	transfer RNA	AW,CW

mol_id	molecule	chains
22	messenger RNA	AV,CV

mol_id	molecule	chains
23	Elongation factor G	AY,CY

mol_id	molecule	chains
24	VIOMYCIN	AU,CU

mol_id	molecule	chains
25	50S ribosomal protein L1	BC,DC

mol_id	molecule	chains
26	50S ribosomal protein L2	BD,DD

mol_id	molecule	chains
27	50S ribosomal protein L3	BE,DE

mol_id	molecule	chains
28	50S ribosomal protein L4	BF,DF

mol_id	molecule	chains
29	50S ribosomal protein L5	BG,DG

mol_id	molecule	chains
30	50S ribosomal protein L6	BH,DH

mol_id	molecule	chains
31	50S RIBOSOMAL PROTEIN L10	BJ,DJ

mol_id	molecule	chains
32	50S ribosomal protein L11	BK,DK

mol_id	molecule	chains
33	50S ribosomal protein L13	BN,DN

mol_id	molecule	chains
34	50S ribosomal protein L14	BO,DO

mol_id	molecule	chains
35	50S ribosomal protein L15	BP,DP

mol_id	molecule	chains
36	50S ribosomal protein L16	BQ,DQ

mol_id	molecule	chains
37	50S ribosomal protein L17	BR,DR

mol_id	molecule	chains
38	50S ribosomal protein L18	BS,DS

mol_id	molecule	chains
39	50S ribosomal protein L19	BT,DT

mol_id	molecule	chains
40	50S ribosomal protein L20	BU,DU

mol_id	molecule	chains
41	50S ribosomal protein L21	BV,DV

mol_id	molecule	chains
42	50S ribosomal protein L22	BW,DW

mol_id	molecule	chains
43	50S ribosomal protein L23	BX,DX

mol_id	molecule	chains
44	50S ribosomal protein L24	BY,DY

mol_id	molecule	chains
45	50S ribosomal protein L25	BZ,DZ

mol_id	molecule	chains
46	50S ribosomal protein L27	B0,D0

mol_id	molecule	chains
47	50S ribosomal protein L29	B2,D2

mol_id	molecule	chains
48	50S ribosomal protein L30	B3,D3

mol_id	molecule	chains
49	50S ribosomal protein L32	B5,D5

mol_id	molecule	chains
50	50S ribosomal protein L33	B6,D6

mol_id	molecule	chains
51	50S ribosomal protein L34	B7,D7

mol_id	molecule	chains
52	50S ribosomal protein L35	B8,D8

mol_id	molecule	chains
53	50S ribosomal protein L36	B9,D9

mol_id	molecule	chains
54	50S ribosomal protein L7/L12	Be,De

mol_id	molecule	chains
55	50S RIBOSOMAL PROTEIN L7/L12	Bf,Bg,Df,Dg

mol_id	molecule	chains
56	50S RIBOSOMAL PROTEIN L7/L12	Bh,Dh

mol_id	molecule	chains
57	50S ribosomal protein L28	B1,D1

mol_id	molecule	chains
58	50S ribosomal protein L31	B4,D4

mol_id	molecule	chains
59	23S ribosomal RNA	BA,DA

mol_id	molecule	chains
60	5S ribosomal RNA	BB,DB

Source :

mol_id	organism_scientific
1	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
2	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
3	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
4	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
5	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
6	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
7	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
8	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
9	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
10	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
11	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
12	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
13	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
14	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
15	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
16	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
17	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
18	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
19	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
20	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
21	Escherichia coli (taxid:562)

mol_id	organism_scientific
22	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
23	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
24	Streptomyces (taxid:1883)

mol_id	organism_scientific
25	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
26	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
27	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
28	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
29	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
30	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
31	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
32	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
33	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
34	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
35	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
36	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
37	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
38	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
39	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
40	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
41	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
42	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
43	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
44	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
45	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
46	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
47	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
48	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
49	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
50	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
51	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
52	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
53	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
54	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
55	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
56	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
57	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
58	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
59	Thermus thermophilus (taxid:262724)
	strain: HB27

mol_id	organism_scientific
60	Thermus thermophilus (taxid:262724)
	strain: HB27

Authors :

Zhou, J., Lancaster, L., Donohue, J.P., Noller, H.F.

Keywords :

FUSIDIC ACID GDP, CHIMERIC HYBRID STATE RIBOSOME, RIBOSOME, TRANSLOCATION INTERMEDIATE, EF-G, MRNA, TRNA, RIBOSOME-ANTIBIOTIC complex

Exp. method :

X-RAY DIFFRACTION ( 3.5 Å )

Citation :

Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation.

Zhou, J.,Lancaster, L.,Donohue, J.P. et al.
(2013) Science 340 : 1236086 - 1236086

PubMed: 23812722
DOI: 10.1126/science.1236086

Chain :	AB, CB
UniProt :	P62662 (RS2_THET2)
Reaction :	-

Chain :	AC, CC
UniProt :	P62663 (RS3_THET2)
Reaction :	-

Chain :

AD, CD

UniProt :

P62664 (RS4_THET2)

Cofactor:	Evidence:	Note:
Reaction :	-
Zn(2+)	ECO:0000250	Binds 1 zinc ion per subunit.

Chain :	AE, CE
UniProt :	P62665 (RS5_THET2)
Reaction :	-

Chain :	AF, CF
UniProt :	P62666 (RS6_THET2)
Reaction :	-

Chain :	AG, CG
UniProt :	P62667 (RS7_THET2)
Reaction :	-

Chain :	AH, CH
UniProt :	P62668 (RS8_THET2)
Reaction :	-

Chain :	AI, CI
UniProt :	P62669 (RS9_THET2)
Reaction :	-

Chain :	AJ, CJ
UniProt :	P62653 (RS10_THET2)
Reaction :	-

Chain :	AK, CK
UniProt :	P62654 (RS11_THET2)
Reaction :	-

Chain :	AL, CL
UniProt :	P61941 (RS12_THET2)
Reaction :	-

Chain :	AM, CM
UniProt :	P62655 (RS13_THET2)
Reaction :	-

Chain :

AN, CN

UniProt :

P62656 (RS14Z_THET2)

Cofactor:	Evidence:	Note:
Reaction :	-
Zn(2+)	ECO:0000255 \| HAMAP-Rule:MF_01364	Binds 1 zinc ion per subunit.

Chain :	AO, CO
UniProt :	P62657 (RS15_THET2)
Reaction :	-

Chain :	AP, CP
UniProt :	P62238 (RS16_THET2)
Reaction :	-

Chain :	AQ, CQ
UniProt :	P62658 (RS17_THET2)
Reaction :	-

Chain :	AR, CR
UniProt :	P62659 (RS18_THET2)
Reaction :	-

Chain :	AS, CS
UniProt :	P62660 (RS19_THET2)
Reaction :	-

Chain :	AT, CT
UniProt :	P62661 (RS20_THET2)
Reaction :	-

Chain :	AY, CY
UniProt :	Q72I01 (EFG_THET2)
Reaction :	-

Chain :	BC, DC
UniProt :	Q72GV9 (RL1_THET2)
Reaction :	-

Chain :	BD, DD
UniProt :	Q72I07 (RL2_THET2)
Reaction :	-

Chain :	BE, DE
UniProt :	Q72I04 (RL3_THET2)
Reaction :	-

Chain :	BF, DF
UniProt :	Q72I05 (RL4_THET2)
Reaction :	-

Chain :	BG, DG
UniProt :	Q72I16 (RL5_THET2)
Reaction :	-

Chain :	BH, DH
UniProt :	Q72I19 (RL6_THET2)
Reaction :	-

Chain :	BK, DK
UniProt :	P62442 (RL11_THET2)
Reaction :	-

Chain :	BN, DN
UniProt :	Q72IN1 (RL13_THET2)
Reaction :	-

Chain :	BO, DO
UniProt :	Q72I14 (RL14_THET2)
Reaction :	-

Chain :	BP, DP
UniProt :	Q72I23 (RL15_THET2)
Reaction :	-

Chain :	BQ, DQ
UniProt :	Q72I11 (RL16_THET2)
Reaction :	-

Chain :	BR, DR
UniProt :	Q72I33 (RL17_THET2)
Reaction :	-

Chain :	BS, DS
UniProt :	Q72I20 (RL18_THET2)
Reaction :	-

Chain :	BT, DT
UniProt :	Q72JU9 (RL19_THET2)
Reaction :	-

Chain :	BU, DU
UniProt :	Q72L76 (RL20_THET2)
Reaction :	-

Chain :	BV, DV
UniProt :	Q72HR2 (RL21_THET2)
Reaction :	-

Chain :	BW, DW
UniProt :	Q72I09 (RL22_THET2)
Reaction :	-

Chain :	BX, DX
UniProt :	Q72I06 (RL23_THET2)
Reaction :	-

Chain :	BY, DY
UniProt :	Q72I15 (RL24_THET2)
Reaction :	-

Chain :	BZ, DZ
UniProt :	Q72IA7 (RL25_THET2)
Reaction :	-

Chain :	B0, D0
UniProt :	Q72HR3 (RL27_THET2)
Reaction :	-

Chain :	B2, D2
UniProt :	Q72I12 (RL29_THET2)
Reaction :	-

Chain :	B3, D3
UniProt :	Q72I22 (RL30_THET2)
Reaction :	-

Chain :	B5, D5
UniProt :	P62652 (RL32_THET2)
Reaction :	-

Chain :	B6, D6
UniProt :	Q72GW3 (RL33_THET2)
Reaction :	-

Chain :	B7, D7
UniProt :	P80340 (RL34_THET8)
Reaction :	-

Chain :	B8, D8
UniProt :	Q72L77 (RL35_THET2)
Reaction :	-

Chain :	B9, D9
UniProt :	Q72I28 (RL36_THET2)
Reaction :	-

Chain :	Be, De
UniProt :	Q72GS2 (RL7_THET2)
Reaction :	-

Chain :	B1, D1
UniProt :	Q72G84 (RL28_THET2)
Reaction :	-

Chain :

B4, D4

UniProt :

Q72JR0 (RL31_THET2)

Cofactor:	Evidence:	Note:
Reaction :	-
Zn(2+)	ECO:0000255 \| HAMAP-Rule:MF_00501	Binds 1 zinc ion per subunit.

PDB ID: 4V9L

Hetero Atom Contents

Structure summary

Reaction