SMTL ID : 8e32.1

E. coli 50S ribosome bound to compound streptogramin analogs SA1 and SB1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x UCX: (3R,4R,5E,10E,12E,14S,16R,23S,26aR)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-yn-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione(Non-functional Binders)

UCX.1: 14 residues within 4Å: Chain A: G.2061, A.2062, C.2063, A.2439, A.2451, C.2452, A.2503, U.2504, G.2505, U.2506, U.2585, U.2586, A.2602 Ligands: UDF.2 No protein-ligand interaction detected (PLIP)

1 x UDF: ~{N}-[(3~{S},6~{S},12~{R},15~{S},16~{R},19~{S},22~{S},24~{R})-12-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethyl]-4,16-dimethyl-24-oxidanyl-2,5,11,14,18,21-hexakis(oxidanylidene)-19-phenyl-3-(phenylmethyl)-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide(Non-functional Binders)

UDF.2: 11 residues within 4Å: Chain A: U.1782, A.2058, A.2059, A.2062, G.2505, U.2585, U.2586, U.2609, C.2610, C.2611 Ligands: UCX.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takahashi, Y. et al., Potential for clicked streptogramin analogs. To Be Published

Release Date

2023-06-28

Peptides

50S ribosomal protein L2: C
50S ribosomal protein L15: D
50S ribosomal protein L4: E
50S ribosomal protein L3: F
50S ribosomal protein L13: G
50S ribosomal protein L22: H
50S ribosomal protein L32: I
50S ribosomal protein L34: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
K

D
L

E
M

F
N

G
O

H
P

I
Q

J
R

50S ribosomal protein L2

50S ribosomal protein L15

50S ribosomal protein L4

50S ribosomal protein L3

50S ribosomal protein L13

50S ribosomal protein L22

50S ribosomal protein L32

50S ribosomal protein L34

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