9njf.1 | SWISS-MODEL Template Library

SMTL ID : 9njf.1

E. coli pre-elongation complex without an A-site tRNA with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation

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 U- U- G- A- A- A: mRNA(Non-functional Binders)

124 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

1 x ZN: ZINC ION(Non-covalent)

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.127:	15 residues within 4Å: Ligands: NA.129 Chain a: F.11, N.36, G.37, S.38, G.39, K.40, S.41, T.42, K.434, V.438, S.440, G.441, G.442, E.443 10 PLIP interactions: 10 interactions with chain a Hydrogen bonds: a:A.35, a:S.38, a:G.39, a:K.40, a:S.41, a:T.42, a:S.440, a:G.442 Salt bridges: a:K.40, a:K.40
ATP.128:	14 residues within 4Å: Ligands: NA.130 Chain a: A.157, F.329, T.353, N.354, G.355, V.356, G.357, K.358, S.359, T.360, Q.389, Q.464, H.493 11 PLIP interactions: 11 interactions with chain a Hydrogen bonds: a:G.355, a:G.355, a:V.356, a:G.357, a:S.359, a:T.360, a:Q.389, a:Q.389 Salt bridges: a:H.493 pi-Stacking: a:F.329, a:F.329

2 x NA: SODIUM ION(Non-functional Binders)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Singh, S. et al., E. coli pre-elongation complex without an A-site tRNA with EQ2-YbiT in Non-hydrolytic 1/PtIM(a) conformation. To Be Published

Release Date

2025-04-02

Peptides

Large ribosomal subunit protein uL1: A
Large ribosomal subunit protein uL10: B
Large ribosomal subunit protein uL11: C
Large ribosomal subunit protein uL13: D
Large ribosomal subunit protein uL14: E
50S ribosomal protein L15: F
50S ribosomal protein L16: G
Large ribosomal subunit protein bL17: H
Large ribosomal subunit protein uL18: I
50S ribosomal protein L19: J
50S ribosomal protein L2: K
Large ribosomal subunit protein bL20: L
Large ribosomal subunit protein bL21: M
Large ribosomal subunit protein uL22: N
Large ribosomal subunit protein uL23: O
Large ribosomal subunit protein uL24: P
Large ribosomal subunit protein bL25: Q
50S ribosomal protein L27: R
50S ribosomal protein L28: S
Large ribosomal subunit protein uL29: T
50S ribosomal protein L3: U
50S ribosomal protein L30: V
Large ribosomal subunit protein bL31: W
50S ribosomal protein L32: X
Large ribosomal subunit protein bL33: Y
50S ribosomal protein L34: Z
Large ribosomal subunit protein bL35: 0
50S ribosomal protein L36: 1
Large ribosomal subunit protein uL4: 2
50S ribosomal protein L5: 3
Large ribosomal subunit protein uL6: 4
Large ribosomal subunit protein bL9: 5
Probable ATP-binding protein YbiT: a
Small ribosomal subunit protein uS2: b
Small ribosomal subunit protein uS3: c
30S ribosomal protein S4: d
Small ribosomal subunit protein uS5: e
30S ribosomal protein S6, non-modified isoform: f
30S ribosomal protein S7: g
30S ribosomal protein S8: h
Small ribosomal subunit protein uS9: i
30S ribosomal protein S10: j
Small ribosomal subunit protein uS11: k
Small ribosomal subunit protein uS12: l
30S ribosomal protein S13: m
Small ribosomal subunit protein uS14: n
Small ribosomal subunit protein uS15: o
Small ribosomal subunit protein bS16: p
Small ribosomal subunit protein uS17: q
30S ribosomal protein S18: r
30S ribosomal protein S19: s
30S ribosomal protein S20: t
Small ribosomal subunit protein bS21: u

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
10

C
11

D
13

E
14

F
15

G
16

H
17

I
18

J
19

K
2

L
20

M
21

N
22

O
23

P
24

Q
25

R
27

S
28

T
29

U
3

V
30

W
31

X
32

Y
33

Z
34

0
35

1
36

2
4

3
5

4
6

5
9

a
Y

b
sb

c
sc

d
sd

e
se

f
sf

g
sg

h
sh

i
si

j
sj

k
sk

l
sl

m
sm

n
sn

o
so

p
sp

q
sq

r
sr

s
ss

t
st

u
su

Large ribosomal subunit protein uL1

Large ribosomal subunit protein uL10

Large ribosomal subunit protein uL11

Large ribosomal subunit protein uL13

Large ribosomal subunit protein uL14

50S ribosomal protein L15

50S ribosomal protein L16

Large ribosomal subunit protein bL17

Large ribosomal subunit protein uL18

50S ribosomal protein L19

50S ribosomal protein L2

Large ribosomal subunit protein bL20

Large ribosomal subunit protein bL21

Large ribosomal subunit protein uL22

Large ribosomal subunit protein uL23

Large ribosomal subunit protein uL24

Large ribosomal subunit protein bL25

50S ribosomal protein L27

50S ribosomal protein L28

Large ribosomal subunit protein uL29

50S ribosomal protein L3

50S ribosomal protein L30

Large ribosomal subunit protein bL31

50S ribosomal protein L32

Large ribosomal subunit protein bL33

50S ribosomal protein L34

Large ribosomal subunit protein bL35

50S ribosomal protein L36

Large ribosomal subunit protein uL4

50S ribosomal protein L5

Large ribosomal subunit protein uL6

Large ribosomal subunit protein bL9

Probable ATP-binding protein YbiT

Small ribosomal subunit protein uS2

Small ribosomal subunit protein uS3

30S ribosomal protein S4

Small ribosomal subunit protein uS5

30S ribosomal protein S6, non-modified isoform

30S ribosomal protein S7

30S ribosomal protein S8

Small ribosomal subunit protein uS9

30S ribosomal protein S10

Small ribosomal subunit protein uS11

Small ribosomal subunit protein uS12

30S ribosomal protein S13

Small ribosomal subunit protein uS14

Small ribosomal subunit protein uS15

Small ribosomal subunit protein bS16

Small ribosomal subunit protein uS17

30S ribosomal protein S18

30S ribosomal protein S19

30S ribosomal protein S20

Small ribosomal subunit protein bS21

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