SMTL ID : 8vr4.1

Structure of Mycobacterium smegmatis 50S ribosomal subunit bound to HflX and erythromycin:50S-HflX-A-Ery

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-mer

Ligands

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 20 residues within 4Å: Chain C: Y.253, T.254, N.255, A.256, G.257, K.258, S.259, S.260, V.272, E.273, N.274, L.276, F.277, A.278, T.279, T.300, V.301, G.302, D.333, K.370 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:N.255, C:A.256, C:G.257, C:K.258, C:K.258, C:K.258, C:S.259, C:S.260, C:E.273, C:F.277, C:A.278, C:T.279, C:T.279, C:T.279, C:T.279, C:G.302 Salt bridges: C:D.333

1 x ERY: ERYTHROMYCIN A(Non-covalent)

ERY.2: 12 residues within 4Å: Chain 7: U.861, A.2282, A.2283, A.2286, A.2727, G.2729, U.2730, C.2834, U.2835 Chain C: V.198, G.199, T.200 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majumdar, S. et al., HflX-mediated drug resistance through ribosome splitting and rRNA disordering in mycobacteria. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-02-19

Peptides

50S ribosomal protein L30: A
50S Ribosomal Protein L27: B
GTPase HflX: C
50S ribosomal protein L2: E
50S ribosomal protein L3: F
50S Ribosomal Protein L4: G
50S Ribosomal Protein L5: H
50S ribosomal protein L6: I
50S ribosomal protein L9: J
50S ribosomal protein L11: K
50S Ribosomal Protein L13: L
50S ribosomal protein L14: M
50S ribosomal protein L15: N
Large ribosomal subunit protein uL16: 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 L32: 1
50S Ribosomal Protein L33: 2
50S ribosomal protein L34: 3
50S ribosomal protein L35: 4
50S ribosomal protein L36: 5
50S Ribosomal Protein L31: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

E
C

F
D

G
E

H
F

I
G

J
H

K
J

L
K

M
L

N
M

O
N

P
O

Q
P

R
Q

S
R

T
S

U
T

V
U

W
V

X
W

Y
X

Z
Y

0
Z

1
b

2
c

3
d

4
e

5
f

6
g

50S ribosomal protein L30

50S Ribosomal Protein L27

GTPase HflX

50S ribosomal protein L2

50S ribosomal protein L3

50S Ribosomal Protein L4

50S Ribosomal Protein L5

50S ribosomal protein L6

50S ribosomal protein L9

50S ribosomal protein L11

50S Ribosomal Protein L13

50S ribosomal protein L14

50S ribosomal protein L15

Large ribosomal subunit protein uL16

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 L32

50S Ribosomal Protein L33

50S ribosomal protein L34

50S ribosomal protein L35

50S ribosomal protein L36

50S Ribosomal Protein L31

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