SMTL ID : 5kcs.1

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Evernimycin, mRNA, TetM and P-site tRNA at 3.9A resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x EVN: (2R,3R,4R,6S)-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7S,7aR)-6-{[(2S,3R,4R,5S,6R)-2-{[(2R,3S,4S,5S,6S)-6-({(2R,3aS,3a'R,6S,7R,7' R,7aS,7a'S)-7'-[(2,4-dihydroxy-6-methylbenzoyl)oxy]-7-hydroxyoctahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}ox y)-4-hydroxy-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-3-hydroxy-5-methoxy-6-methyltetrahydro-2H-pyran-4- yl]oxy}-4',7-dihydroxy-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-4-{[(2R,4S,5R, 6S)-5-methoxy-4,6-dimethyl-4-nitrotetrahydro-2H-pyran-2-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name)(Non-covalent)

EVN.1: 13 residues within 4Å: Chain A: A.2469, G.2470, A.2471, G.2472, A.2478, U.2479, C.2480, A.2530, A.2534, G.2535, G.2536 Chain O: R.51, R.55 3 PLIP interactions: 3 interactions with chain O Hydrogen bonds: O:R.55 Salt bridges: O:R.51 pi-Cation interactions: O:R.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arenz, S. et al., Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-17

Peptides

50S ribosomal protein L2: C
50S ribosomal protein L3: D
50S ribosomal protein L4: E
50S ribosomal protein L5: F
50S ribosomal protein L6: G
50S ribosomal protein L7/L12: H
50S ribosomal protein L9: I
50S ribosomal protein L10: J
50S ribosomal protein L11: K
50S ribosomal protein L13: L
50S ribosomal protein L14: M
50S ribosomal protein L15: N
50S ribosomal protein L16: O
50S ribosomal protein L17: P
50S ribosomal protein L18: Q
50S ribosomal protein L19: R
50S ribosomal protein L20: S
50S ribosomal protein L21: T
50S ribosomal protein L22: U
50S ribosomal protein L23: V
50S ribosomal protein L24: W
50S ribosomal protein L25: X
50S ribosomal protein L27: Y
50S ribosomal protein L28: Z
50S ribosomal protein L29: 0
50S ribosomal protein L30: 1
50S ribosomal protein L31: 2
50S ribosomal protein L32: 3
50S ribosomal protein L33: 4
50S ribosomal protein L34: 5
50S ribosomal protein L35: 6
50S ribosomal protein L36: 7
30S ribosomal protein S2: 9
30S ribosomal protein S3: a
30S ribosomal protein S4: b
30S ribosomal protein S5: c
30S ribosomal protein S6: d
30S ribosomal protein S7: e
30S ribosomal protein S8: f
30S ribosomal protein S9: g
30S ribosomal protein S10: h
30S ribosomal protein S11: i
30S ribosomal protein S12: j
30S ribosomal protein S13: k
30S ribosomal protein S14: l
30S ribosomal protein S15: m
30S ribosomal protein S16: n
30S ribosomal protein S17: o
30S ribosomal protein S18: p
30S ribosomal protein S19: q
30S ribosomal protein S20: r
30S ribosomal protein S21: s
Tetracycline resistance protein TetM from transposon Tn916: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
1D

D
1E

E
1F

F
1G

G
1H

H
1L

I
1I

J
1J

K
1K

L
1N

M
1O

N
1P

O
1Q

P
1R

Q
1S

R
1T

S
1U

T
1V

U
1W

V
1X

W
1Y

X
1Z

Y
10

Z
11

0
12

1
13

2
14

3
15

4
16

5
17

6
18

7
19

9
1b

a
1c

b
1d

c
1e

d
1f

e
1g

f
1h

g
1i

h
1j

i
1k

j
1l

k
1m

l
1n

m
1o

n
1p

o
1q

p
1r

q
1s

r
1t

s
1u

u
1w

50S ribosomal protein L2

50S ribosomal protein L3

50S ribosomal protein L4

50S ribosomal protein L5

50S ribosomal protein L6

50S ribosomal protein L7/L12

50S ribosomal protein L9

50S ribosomal protein L10

50S ribosomal protein L11

50S ribosomal protein L13

50S ribosomal protein L14

50S ribosomal protein L15

50S ribosomal protein L16

50S ribosomal protein L17

50S ribosomal protein L18

50S ribosomal protein L19

50S ribosomal protein L20

50S ribosomal protein L21

50S ribosomal protein L22

50S ribosomal protein L23

50S ribosomal protein L24

50S ribosomal protein L25

50S ribosomal protein L27

50S ribosomal protein L28

50S ribosomal protein L29

50S ribosomal protein L30

50S ribosomal protein L31

50S ribosomal protein L32

50S ribosomal protein L33

50S ribosomal protein L34

50S ribosomal protein L35

50S ribosomal protein L36

30S ribosomal protein S2

30S ribosomal protein S3

30S ribosomal protein S4

30S ribosomal protein S5

30S ribosomal protein S6

30S ribosomal protein S7

30S ribosomal protein S8

30S ribosomal protein S9

30S ribosomal protein S10

30S ribosomal protein S11

30S ribosomal protein S12

30S ribosomal protein S13

30S ribosomal protein S14

30S ribosomal protein S15

30S ribosomal protein S16

30S ribosomal protein S17

30S ribosomal protein S18

30S ribosomal protein S19

30S ribosomal protein S20

30S ribosomal protein S21

Tetracycline resistance protein TetM from transposon Tn916

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