- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 2.20 Å
- Oligo State
- hetero-1-1-1-1-1-1-1-1-mer
- Ligands
- 1 x YQM: Eravacycline(Non-functional Binders)
YQM.1: 10 residues within 4Å:- Chain A: U.965, G.966, G.1053, C.1054, C.1195, A.1196, A.1197, G.1198
- Ligands: MG.2, MG.16
No protein-ligand interaction detected (PLIP)- 32 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)
MG.2: 2 residues within 4Å:- Chain A: G.966
- Ligands: YQM.1
No protein-ligand interaction detected (PLIP)MG.3: 2 residues within 4Å:- Chain A: G.944, G.945
No protein-ligand interaction detected (PLIP)MG.4: 1 residues within 4Å:- Chain A: U.1224
No protein-ligand interaction detected (PLIP)MG.5: 2 residues within 4Å:- Chain A: C.979, C.980
No protein-ligand interaction detected (PLIP)MG.6: 2 residues within 4Å:- Chain A: A.1110, U.1189
No protein-ligand interaction detected (PLIP)MG.7: 2 residues within 4Å:- Chain A: U.1095, G.1108
No protein-ligand interaction detected (PLIP)MG.8: 4 residues within 4Å:- Chain A: A.1067, G.1068, G.1094, G.1387
No protein-ligand interaction detected (PLIP)MG.9: 2 residues within 4Å:- Chain A: C.1069, U.1085
No protein-ligand interaction detected (PLIP)MG.10: 1 residues within 4Å:- Chain A: C.934
No protein-ligand interaction detected (PLIP)MG.11: 2 residues within 4Å:- Chain A: A.937, A.938
No protein-ligand interaction detected (PLIP)MG.12: 1 residues within 4Å:- Chain A: A.1254
No protein-ligand interaction detected (PLIP)MG.13: 1 residues within 4Å:- Chain H: Q.60
No protein-ligand interaction detected (PLIP)MG.14: 2 residues within 4Å:- Chain A: G.1048
- Chain H: A.2
No protein-ligand interaction detected (PLIP)MG.15: 3 residues within 4Å:- Chain A: G.963, A.964, U.1199
No protein-ligand interaction detected (PLIP)MG.16: 5 residues within 4Å:- Chain A: C.1054, A.1196, A.1197, G.1198
- Ligands: YQM.1
No protein-ligand interaction detected (PLIP)MG.17: 1 residues within 4Å:- Chain A: G.953
No protein-ligand interaction detected (PLIP)MG.18: 2 residues within 4Å:- Chain A: G.1177, G.1181
No protein-ligand interaction detected (PLIP)MG.19: 4 residues within 4Å:- Chain A: G.1053, C.1054, A.1196, A.1197
No protein-ligand interaction detected (PLIP)MG.20: 1 residues within 4Å:- Chain A: C.1200
No protein-ligand interaction detected (PLIP)MG.21: 8 residues within 4Å:- Chain A: C.979, C.980, U.981, U.982, G.1221, G.1222, C.1223
- Ligands: K.35
No protein-ligand interaction detected (PLIP)MG.22: 1 residues within 4Å:- Chain A: G.1370
No protein-ligand interaction detected (PLIP)MG.23: 1 residues within 4Å:- Chain A: C.972
No protein-ligand interaction detected (PLIP)MG.24: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.25: 2 residues within 4Å:- Chain A: C.1303, G.1304
No protein-ligand interaction detected (PLIP)MG.26: 2 residues within 4Å:- Chain A: A.1285, G.1355
No protein-ligand interaction detected (PLIP)MG.27: 3 residues within 4Å:- Chain A: G.1050, C.1051, C.1208
No protein-ligand interaction detected (PLIP)MG.28: 1 residues within 4Å:- Chain A: A.1357
No protein-ligand interaction detected (PLIP)MG.29: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.30: 1 residues within 4Å:- Chain A: G.1013
No protein-ligand interaction detected (PLIP)MG.31: 1 residues within 4Å:- Chain A: U.1291
No protein-ligand interaction detected (PLIP)MG.32: 1 residues within 4Å:- Chain A: A.1311
No protein-ligand interaction detected (PLIP)MG.33: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)- 12 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)
K.34: 5 residues within 4Å:- Chain A: U.1224, A.1225, C.1322
- Chain G: G.99, Q.100
1 PLIP interactions:1 interactions with chain G- Metal complexes: G:Q.100
K.35: 5 residues within 4Å:- Chain A: A.978, C.979, G.1222, C.1322
- Ligands: MG.21
No protein-ligand interaction detected (PLIP)K.36: 5 residues within 4Å:- Chain A: G.1053, G.1058, C.1059, G.1198, U.1199
No protein-ligand interaction detected (PLIP)K.37: 4 residues within 4Å:- Chain A: G.976, C.1359, G.1361, A.1362
No protein-ligand interaction detected (PLIP)K.38: 5 residues within 4Å:- Chain A: A.949, G.971, G.1233, C.1234, U.1364
No protein-ligand interaction detected (PLIP)K.39: 5 residues within 4Å:- Chain A: U.1073, G.1074, A.1082, U.1083, G.1084
No protein-ligand interaction detected (PLIP)K.40: 6 residues within 4Å:- Chain A: C.1051, U.1052, C.1200, U.1205, G.1206, G.1207
No protein-ligand interaction detected (PLIP)K.41: 3 residues within 4Å:- Chain A: A.1319, C.1322, G.1323
No protein-ligand interaction detected (PLIP)K.42: 3 residues within 4Å:- Chain A: C.1303, G.1304, G.1305
No protein-ligand interaction detected (PLIP)K.43: 4 residues within 4Å:- Chain A: U.943, G.944, U.1232, G.1233
No protein-ligand interaction detected (PLIP)K.44: 4 residues within 4Å:- Chain A: U.943, G.944, G.945, G.1337
No protein-ligand interaction detected (PLIP)K.45: 4 residues within 4Å:- Chain A: U.1330
- Chain G: T.20, I.22, V.25
5 PLIP interactions:3 interactions with chain G, 2 Ligand-Water interactions- Metal complexes: G:T.20, G:I.22, G:V.25, H2O.2, H2O.14
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Paternoga, H. et al., Structural conservation of antibiotic interaction with ribosomes. Nat.Struct.Mol.Biol. (2023)
- Release Date
- 2023-08-02
- Peptides
- 30S ribosomal protein S2: B
Small ribosomal subunit protein uS3: C
30S ribosomal protein S7: D
Small ribosomal subunit protein uS9: E
Small ribosomal subunit protein uS10: F
Small ribosomal subunit protein uS13: G
Small ribosomal subunit protein uS14: H
Small ribosomal subunit protein uS19: I - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:B
BC
CD
GE
IF
JG
MH
NI
S
SMTL ID : 8cf8.1
Eravacycline bound to the 30S head
30S ribosomal protein S2
Small ribosomal subunit protein uS3
30S ribosomal protein S7
Small ribosomal subunit protein uS9
Small ribosomal subunit protein uS10
Small ribosomal subunit protein uS13
Small ribosomal subunit protein uS14
Small ribosomal subunit protein uS19
Related Entries With Identical Sequence
3j9y.1 | 3j9z.1 | 3ja1.1 | 3jbu.1 | 3jbv.1 | 3jcd.1 | 3jce.1 | 3jcj.1 | 3jcn.1 | 3w1y.1 | 3w1y.2 | 4adv.1 | 4v4h.1 | 4v4h.2 | 4v4q.1 | 4v4q.2 | 4v50.1 | 4v50.2 | 4v52.1 | 4v52.2 | 4v53.1 | 4v53.2 | 4v54.1 | 4v54.2 | 4v55.1 | 4v55.2 | 4v56.1 | 4v56.2 | 4v57.1 | 4v57.2 more...less...4v5b.1 | 4v5b.2 | 4v5y.1 | 4v5y.2 | 4v64.1 | 4v64.2 | 4v65.1 | 4v66.1 | 4v6c.1 | 4v6c.2 | 4v6d.1 | 4v6d.2 | 4v6e.1 | 4v6e.2 | 4v6k.1 | 4v6l.1 | 4v6m.1 | 4v6n.1 | 4v6o.1 | 4v6p.1 | 4v6q.1 | 4v6r.1 | 4v6s.1 | 4v6v.1 | 4v6y.1 | 4v6z.1 | 4v70.1 | 4v71.1 | 4v72.1 | 4v73.1 | 4v74.1 | 4v75.1 | 4v76.1 | 4v77.1 | 4v78.1 | 4v79.1 | 4v7a.1 | 4v7b.1 | 4v7c.1 | 4v7d.1 | 4v7i.1 | 4v85.1 | 4v89.1 | 4v9c.1 | 4v9c.2 | 4v9o.1 | 4v9o.2 | 4v9o.3 | 4v9o.4 | 4v9p.1 | 4v9p.2 | 4v9p.3 | 4v9p.4 | 4woi.1 | 4woi.2 | 4www.1 | 4www.2 | 5afi.1 | 5h5u.1 | 5iqr.1 | 5jte.1 | 5ju8.1 | 5kcr.1 | 5kcs.1 | 5kps.1 | 5kpv.1 | 5kpw.1 | 5kpx.1 | 5l3p.1 | 5mdv.1 | 5mdw.1 | 5mdy.1 | 5mdz.1 | 5me0.1 | 5me1.1 | 5my1.1 | 5nwy.1 | 5u4i.1 | 5u4j.1 | 5u9f.1 | 5u9g.1 | 5uz4.1 | 6by1.1 | 6by1.2 | 6c4i.1 | 6dnc.1 | 6ogf.1 | 6ogg.1 | 6ogi.1 | 6om6.1 | 6q98.1 | 6szs.1 | 6tbv.1 | 6tc3.1 | 6vwl.1 | 6vwm.1 | 6vwn.1 | 6vyx.15 | 6vyx.17 | 6vyx.21 | 6vyx.23 | 6vyx.24 | 6vyx.27 | 6vyx.31 | 6vyx.32 | 6w6k.1 | 6w77.1 | 6w7m.1 | 6w7n.1 | 6ysr.1 | 6yss.1 | 6yst.1 | 6ysu.1 | 6ztj.1 | 6ztj.2 | 6ztj.8 | 6ztj.9 | 6ztj.12 | 6ztj.13 | 6ztj.18 | 6ztl.1 | 6ztm.1 | 6ztn.1 | 6ztn.2 | 6ztn.8 | 6ztn.9 | 6ztn.12 | 6ztn.13 | 6ztn.18 | 6zto.1 | 6ztp.1 | 6zu1.1 | 7af3.1 | 7af5.1 | 7af8.1 | 7afa.1 | 7afd.1 | 7afh.1 | 7afk.1 | 7afn.1 | 7boe.1 | 7boh.1 | 7cpj.1 | 7d6z.1 | 7d80.1 | 7k00.1 | 7n1p.1 | 7n2c.1 | 7n2u.1 | 7n2v.1 | 7n30.1 | 7n31.1 | 7nar.1 | 7nat.1 | 7nau.1 | 7nav.1 | 7nax.1 | 7nwt.1 | 7o19.1 | 7o1a.1 | 7o1c.1 | 7oe0.1 | 7oe1.1 | 7oiz.1 | 7oj0.1 | 7otc.1 | 7p3k.1 | 7pjs.1 | 7pjt.1 | 7pju.1 | 7pjv.1 | 7pjw.1 | 7pjx.1 | 7pjy.1 | 7pjz.1 | 7q4k.1 | 7qg8.1 | 7qgn.1 | 7qgr.1 | 7s1g.1 | 7s1h.1 | 7s1i.1 | 7s1j.1 | 7s1k.1 | 7sa4.1 | 7ug7.1 | 7y7c.1 | 7y7d.1 | 7y7e.1 | 7y7f.1 | 7y7g.1 | 7y7h.1 | 8a3l.1 | 8akn.1 | 8am9.1 | 8aye.1 | 8b0x.1 | 8b7y.1 | 8bf7.1 | 8bge.1 | 8bgh.1 | 8bh4.1 | 8bhj.1 | 8bhl.1 | 8bhn.1 | 8bhp.1 | 8bil.1 | 8bim.1 | 8ca7.1 | 8cai.1 | 8caz.1 | 8cf1.1 | 8cgi.1 | 8cgj.1 | 8eiu.1 | 8ekc.1 | 8emm.1 | 8eyq.1 | 8eyt.1 | 8fiz.1 | 8fto.1 | 8fzd.1 | 8fze.1 | 8fzf.1 | 8fzg.1 | 8fzh.1 | 8fzi.1 | 8fzj.1 | 8g6w.1 | 8g7p.1 | 8g7q.1 | 8g7r.1 | 8g7s.1 | 8hsp.1 | 8htz.1 | 8hu1.1 | 8ifb.1 | 8ifc.1 | 8k3o.1 | 8k4e.1 | 8p16.1 | 8p17.1 | 8p18.1 | 8peg.1 | 8phj.1 | 8pkl.1 | 8pva.1 | 8q4f.1 | 8qbt.1 | 8qk7.1 | 8qoa.1 | 8r6c.1 | 8r8m.1 | 8syl.1 | 8vs9.1 | 8vsa.1 | 8yuo.1 | 8yup.1 | 8yuq.1 | 8yur.1 | 8yus.1 | 9ax7.1 | 9cg5.1 | 9cg6.1 | 9cg7.1 | 9fbv.1 | 9gr1.1 | 9gup.1 | 9guq.1 | 9gus.1 | 9gut.1 | 9guu.1 | 9guv.1 | 9guw.1 | 9gux.1