PDBsum entry 4ioa

Ribosome/ribosome inhibitor

PDB id: 4ioa

Contents

Protein chains

240 a.a.

205 a.a.

197 a.a.

177 a.a.

171 a.a.

71 a.a.

142 a.a.

134 a.a.

141 a.a.

136 a.a.

113 a.a.

104 a.a.

108 a.a.

117 a.a.

94 a.a.

127 a.a.

93 a.a.

110 a.a.

175 a.a.

84 a.a.

72 a.a.

66 a.a.

55 a.a.

58 a.a.

53 a.a.*

46 a.a.*

63 a.a.*

37 a.a.

DNA/RNA

Ligands

1F3

Metals

_MG ×35

* C-alpha coords only

PDB id:

4ioa

Name:

Ribosome/ribosome inhibitor

Title:

Crystal structure of compound 4e bound to large ribosomal subunit (50s) from deinococcus radiodurans

Structure:

23s ribosomal RNA. Chain: x. 5s ribosomal RNA. Chain: y. 50s ribosomal protein l2. Chain: a. 50s ribosomal protein l3. Chain: b. 50s ribosomal protein l4.

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Organism_taxid: 1299

Resolution:

3.20Å R-factor: 0.197 R-free: 0.230

Authors:

S.Han,E.S.Marr

Key ref:

T.V.Magee et al. (2013). Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates. Bioorg Med Chem Lett, 23, 1727-1731. PubMed id: 23414806 DOI: 10.1016/j.bmcl.2013.01.067

Date:

07-Jan-13 Release date: 06-Mar-13

Protein chain

Q9RXJ9  (RL2_DEIRA) -  Large ribosomal subunit protein uL2 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 275 a.a.

Struc: 240 a.a.

Protein chain

Q9RXK2  (RL3_DEIRA) -  Large ribosomal subunit protein uL3 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 211 a.a.

Struc: 205 a.a.

Protein chain

Q9RXK1  (RL4_DEIRA) -  Large ribosomal subunit protein uL4 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 205 a.a.

Struc: 197 a.a.

Protein chain

Q9RXJ0  (RL5_DEIRA) -  Large ribosomal subunit protein uL5 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 180 a.a.

Struc: 177 a.a.

Protein chain

Q9RSL3  (RL6_DEIRA) -  Large ribosomal subunit protein uL6 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 185 a.a.

Struc: 171 a.a.

Protein chain

Q9RSS7  (RL11_DEIRA) -  Large ribosomal subunit protein uL11 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 144 a.a.

Struc: 71 a.a.

Protein chain

Q9RXY1  (RL13_DEIRA) -  Large ribosomal subunit protein uL13 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 174 a.a.

Struc: 142 a.a.

Protein chain

Q9RXJ2  (RL14_DEIRA) -  Large ribosomal subunit protein uL14 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 134 a.a.

Struc: 134 a.a.

Protein chain

Q9RSK9  (RL15_DEIRA) -  Large ribosomal subunit protein uL15 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 156 a.a.

Struc: 141 a.a.

Protein chain

Q9RXJ5  (RL16_DEIRA) -  Large ribosomal subunit protein uL16 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 141 a.a.

Struc: 136 a.a.

Protein chain

Q9RSJ5  (RL17_DEIRA) -  Large ribosomal subunit protein bL17 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 116 a.a.

Struc: 113 a.a.

Protein chain

Q9RSL2  (RL18_DEIRA) -  Large ribosomal subunit protein uL18 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 114 a.a.

Struc: 104 a.a.

Protein chain

Q9RWB4  (RL19_DEIRA) -  Large ribosomal subunit protein bL19 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 166 a.a.

Struc: 108 a.a.

Protein chain

Q9RSW7  (RL20_DEIRA) -  Large ribosomal subunit protein bL20 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 118 a.a.

Struc: 117 a.a.

Protein chain

Q9RY64  (RL21_DEIRA) -  Large ribosomal subunit protein bL21 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 100 a.a.

Struc: 94 a.a.

Protein chain

Q9RXJ7  (RL22_DEIRA) -  Large ribosomal subunit protein uL22 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 134 a.a.

Struc: 127 a.a.

Protein chain

Q9RXK0  (RL23_DEIRA) -  Large ribosomal subunit protein uL23 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 95 a.a.

Struc: 93 a.a.

Protein chain

Q9RXJ1  (RL24_DEIRA) -  Large ribosomal subunit protein uL24 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 115 a.a.

Struc: 110 a.a.

Protein chain

Q9RX88  (RL25_DEIRA) -  Large ribosomal subunit protein bL25 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 237 a.a.

Struc: 175 a.a.

Protein chain

Q9RY65  (RL27_DEIRA) -  Large ribosomal subunit protein bL27 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 91 a.a.

Struc: 84 a.a.

Protein chain

Q9RRG8  (RL28_DEIRA) -  Large ribosomal subunit protein bL28 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 81 a.a.

Struc: 72 a.a.

Protein chain

Q9RXJ4  (RL29_DEIRA) -  Large ribosomal subunit protein uL29 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 67 a.a.

Struc: 66 a.a.

Protein chain

Q9RSL0  (RL30_DEIRA) -  Large ribosomal subunit protein uL30 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 55 a.a.

Struc: 55 a.a.

Protein chain

P49228  (RL32_DEIRA) -  Large ribosomal subunit protein bL32 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 60 a.a.

Struc: 58 a.a.

Protein chain

Q9RSS4  (RL33_DEIRA) -  Large ribosomal subunit protein bL33 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 55 a.a.

Struc: 53 a.a.

Protein chain

Q9RSH2  (RL34_DEIRA) -  Large ribosomal subunit protein bL34 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 47 a.a.

Struc: 46 a.a.

Protein chain

Q9RSW6  (RL35_DEIRA) -  Large ribosomal subunit protein bL35 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 66 a.a.

Struc: 63 a.a.

Protein chain

Q9RSK0  (RL36_DEIRA) -  Large ribosomal subunit protein bL36 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 37 a.a.

Struc: 37 a.a.

DNA/RNA chains

G-G-U-C-A-A-G-A-U-A-G-U-A-A-G-G-G-U-C-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-G-C- ... 2686 bases

C-A-C-C-C-C-C-G-U-G-C-C-C-A-U-A-G-C-A-C-U-G-U-G-G-A-A-C-C-A-C-C-C-C-A-C-C-C-C- 122 bases

reference

DOI no: 10.1016/j.bmcl.2013.01.067

Bioorg Med Chem Lett 23:1727-1731 (2013)

PubMed id: 23414806

Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.

T.V.Magee, S.Han, S.P.McCurdy, T.T.Nguyen, K.Granskog, E.S.Marr, B.A.Maguire, M.D.Huband, J.M.Chen, T.A.Subashi, V.Shanmugasundaram.

ABSTRACT

A novel series of 3-O-carbamoyl erythromycin A derived analogs, labeled carbamolides, with activity versus resistant bacterial isolates of staphylococci (including macrolide and oxazolidinone resistant strains) and streptococci are reported. An (R)-2-aryl substituent on a pyrrolidine carbamate appeared to be critical for achieving potency against resistant strains. Crystal structures showed a distinct aromatic interaction between the (R)-2-aryl (3-pyridyl for 4d) substituent on the pyrrolidine and G2484 (G2505, Escherichia coli) of the Deinococcus radiodurans 50S ribosome (3.2Å resolution).