1n8r.1 | SWISS-MODEL Template Library

SMTL ID : 1n8r.1

Structure of large ribosomal subunit in complex with virginiamycin M

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

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-mer

Ligands

1 x VIR: VIRGINIAMYCIN M1(Non-functional Binders)

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

1 x K: POTASSIUM ION(Non-covalent)

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

22 x CL: CHLORIDE ION(Non-functional Binders)

5 x CD: CADMIUM ION(Non-covalent)

CD.214:	1 residues within 4Å: Chain P: H.40 2 PLIP interactions: 1 interactions with chain P, 1 Ligand-Water interactions Metal complexes: P:H.40, H₂O.275
CD.223:	4 residues within 4Å: Chain V: C.6, C.9, C.32, C.36 No protein-ligand interaction detected (PLIP)
CD.227:	4 residues within 4Å: Chain 0: C.30, C.33, C.48, C.51 No protein-ligand interaction detected (PLIP)
CD.228:	4 residues within 4Å: Chain 1: C.19, C.22, C.34, C.37 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.19, 1:C.22, 1:C.34, 1:C.37
CD.231:	5 residues within 4Å: Chain 3: C.11, H.13, C.14, C.71, C.74 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hansen, J. et al., Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit. J.Mol.Biol. (2003)

Release Date

2003-07-22

Peptides

50S ribosomal protein L2P: C
50S ribosomal protein L3P: D
50S ribosomal protein L4E: E
50S ribosomal protein L5P: F
50S ribosomal protein L6P: G
50S ribosomal protein L7Ae: H
Acidic ribosomal protein P0 homolog: I
50S ribosomal protein L10e: J
50S ribosomal protein L13P: K
50S ribosomal protein L14P: L
50S ribosomal protein L15P: M
50S ribosomal protein L15E: N
50S ribosomal protein L18P: O
50S ribosomal protein L18E: P
50S ribosomal protein L19E: Q
50S ribosomal protein L21e: R
50S ribosomal protein L22P: S
50S ribosomal protein L23P: T
50S ribosomal protein L24P: U
50S ribosomal protein L24E: V
50S ribosomal protein L29P: W
50S ribosomal protein L30P: X
50S ribosomal protein L31E: Y
50S ribosomal protein L32E: Z
50S ribosomal protein L37AE: 0
50S ribosomal protein L37e: 1
50S ribosomal protein L39e: 2
50S ribosomal protein L44E: 3

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
1

1
2

2
3

3
4

50S ribosomal protein L2P

50S ribosomal protein L3P

50S ribosomal protein L4E

50S ribosomal protein L5P

50S ribosomal protein L6P

50S ribosomal protein L7Ae

Acidic ribosomal protein P0 homolog

50S ribosomal protein L10e

50S ribosomal protein L13P

50S ribosomal protein L14P

50S ribosomal protein L15P

50S ribosomal protein L15E

50S ribosomal protein L18P

50S ribosomal protein L18E

50S ribosomal protein L19E

50S ribosomal protein L21e

50S ribosomal protein L22P

50S ribosomal protein L23P

50S ribosomal protein L24P

50S ribosomal protein L24E

50S ribosomal protein L29P

50S ribosomal protein L30P

50S ribosomal protein L31E

50S ribosomal protein L32E

50S ribosomal protein L37AE

50S ribosomal protein L37e

50S ribosomal protein L39e

50S ribosomal protein L44E

Related Entries With Identical Sequence

1jj2.1 | 1k73.1 | 1k8a.1 | 1k9m.1 | 1kc8.1 | 1kd1.1 | 1kqs.1 | 1m1k.1 | 1m90.1 | 1nji.1 | 1q7y.1 | 1q81.1 | 1q82.1 | 1q86.1 | 1qvf.1 | 1qvg.1 | 1s72.1 | 1vq4.1 | 1vq5.1 | 1vq6.1 | 1vq7.1 | 1vq8.1 | 1vq9.1 | 1vqk.1 | 1vql.1 | 1vqm.1 | 1vqn.1 | 1vqo.1 | 1vqp.1 | 1w2b.1 more...