- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.33 Å
- Oligo State
- hetero-1-1-1-mer
- Ligands
- 1 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
GTP.1: 28 residues within 4Å:- Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, E.183, N.206, Y.224, L.227, N.228, I.231
- Chain B: K.252
- Ligands: MG.2
32 PLIP interactions:26 interactions with chain A, 6 interactions with chain B- Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228
- Water bridges: A:S.140, A:S.140, A:G.142, A:E.183, B:K.252, B:K.252, B:K.252, B:K.252, B:K.252
- pi-Stacking: A:Y.224, A:Y.224
- Salt bridges: B:K.252
- 1 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 5 residues within 4Å:- Chain A: Q.11, E.71, D.98
- Chain B: K.252
- Ligands: GTP.1
No protein-ligand interaction detected (PLIP)- 5 x SO4: SULFATE ION(Non-functional Binders)
SO4.3: 6 residues within 4Å:- Chain A: V.177, R.221, P.222, T.223, Y.224
- Chain B: Q.245
4 PLIP interactions:3 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:V.177, A:Y.224, B:Q.245
- Salt bridges: A:R.221
SO4.5: 3 residues within 4Å:- Chain A: P.175, K.394
- Chain B: N.347
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Salt bridges: A:K.394
- Hydrogen bonds: B:N.347
SO4.8: 3 residues within 4Å:- Chain B: T.221, G.223, R.276
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:T.221, B:T.221, B:G.223
- Salt bridges: B:R.276
SO4.9: 2 residues within 4Å:- Chain B: K.19, R.276
2 PLIP interactions:2 interactions with chain B- Salt bridges: B:K.19, B:R.276
SO4.12: 4 residues within 4Å:- Chain C: V.150, F.161, L.176, Q.177
No protein-ligand interaction detected (PLIP)- 2 x CL: CHLORIDE ION(Non-functional Binders)
CL.4: 3 residues within 4Å:- Chain A: K.336, G.350, F.351
Ligand excluded by PLIPCL.10: 3 residues within 4Å:- Chain A: T.179
- Chain B: K.350, V.351
Ligand excluded by PLIP- 1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.6: 26 residues within 4Å:- Chain B: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229
18 PLIP interactions:18 interactions with chain B- Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:V.175, B:N.204, B:N.204, B:N.226, B:N.226
- Water bridges: B:L.139, B:G.140
- pi-Stacking: B:Y.222, B:Y.222
- 1 x V95: methyl N-(6-benzoyl-1H-benzimidazol-2-yl)carbamate(Non-covalent)
V95.7: 23 residues within 4Å:- Chain A: T.179
- Chain B: I.4, Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, S.239, L.240, L.246, L.250, L.253, M.257, A.314, T.315, V.316, K.350, V.351, A.352, I.368
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:L.246, B:L.253, B:L.253, B:A.314, B:K.350, B:A.352, B:I.368
- Hydrogen bonds: B:N.165, B:E.198, B:V.236, B:S.239
- Water bridges: B:A.254
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.11: 5 residues within 4Å:- Chain B: T.386, R.390, E.412
- Chain C: M.90, W.123
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:R.390, B:R.390, C:W.123
GOL.13: 11 residues within 4Å:- Chain B: R.391, K.392, A.393, F.394, H.396
- Chain C: R.34, L.59, L.64, T.67, Y.68, L.97
5 PLIP interactions:4 interactions with chain C, 1 interactions with chain B- Hydrogen bonds: C:R.34, C:R.34, C:Y.68, C:Y.68, B:R.391
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Oliva, M.A. et al., Effect of Clinically Used Microtubule Targeting Drugs on Viral Infection and Transport Function. Int J Mol Sci (2022)
- Release Date
- 2022-04-06
- Peptides
- Tubulin alpha-1B chain: A
Tubulin beta-3 chain: B
Designed Ankyrin Repeat Protein (DARPIN) D1: C - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
F
SMTL ID : 7odn.1
Crystal structure of TD1-mebendazole complex
Tubulin alpha-1B chain
Tubulin beta-3 chain
Designed Ankyrin Repeat Protein (DARPIN) D1
Related Entries With Identical Sequence
3j8x.1 | 3j8y.1 | 3jak.1 | 3jal.1 | 3jar.1 | 3jas.1 | 3jat.1 | 3jaw.1 | 3ryc.1 | 3ryf.1 | 3ryh.1 | 3ryi.1 | 3ut5.1 | 4eb6.1 | 4f61.1 | 4f6r.1 | 4hna.1 | 4i50.1 | 4iij.1 | 4lnu.1 | 4o2a.1 | 4o2b.1 | 4o4h.1 | 4o4i.1 | 4o4j.1 | 4o4l.1 | 4tuy.1 | 4tv8.1 | 4tv9.1 | 4yj2.1 more...less...4yj3.1 | 4zhq.1 | 4zi7.1 | 4zol.1 | 5bmv.1 | 5ca0.1 | 5eib.1 | 5eyp.1 | 5fnv.1 | 5itz.1 | 5iyz.1 | 5j2t.1 | 5j2u.1 | 5jcb.1 | 5jqg.1 | 5jvd.1 | 5la6.1 | 5lov.1 | 5lxs.1 | 5lxt.1 | 5lyj.1 | 5m7e.1 | 5m7g.1 | 5m8d.1 | 5m8g.1 | 5mf4.1 | 5mio.1 | 5nfz.1 | 5ng1.1 | 5nm5.1 | 5nqt.1 | 5nqu.1 | 5o7a.1 | 5osk.1 | 5ov7.1 | 5s4l.1 | 5s4m.1 | 5s4n.1 | 5s4o.1 | 5s4p.1 | 5s4q.1 | 5s4r.1 | 5s4s.1 | 5s4t.1 | 5s4u.1 | 5s4v.1 | 5s4w.1 | 5s4x.1 | 5s4y.1 | 5s4z.1 | 5s50.1 | 5s51.1 | 5s52.1 | 5s53.1 | 5s54.1 | 5s55.1 | 5s56.1 | 5s57.1 | 5s58.1 | 5s59.1 | 5s5a.1 | 5s5b.1 | 5s5c.1 | 5s5d.1 | 5s5e.1 | 5s5f.1 | 5s5g.1 | 5s5h.1 | 5s5i.1 | 5s5j.1 | 5s5k.1 | 5s5l.1 | 5s5m.1 | 5s5n.1 | 5s5o.1 | 5s5p.1 | 5s5q.1 | 5s5r.1 | 5s5s.1 | 5s5t.1 | 5s5u.1 | 5s5v.1 | 5s5w.1 | 5s5x.1 | 5s5y.1 | 5s5z.1 | 5s60.1 | 5s61.1 | 5s62.1 | 5s63.1 | 5s64.1 | 5s65.1 | 5s66.1 | 5s67.1 | 5sb3.1 | 5sb4.1 | 5sb5.1 | 5sb6.1 | 5sb7.1 | 5sb8.1 | 5sb9.1 | 5sba.1 | 5sbb.1 | 5sbc.1 | 5sbd.1 | 5sbe.1 | 5xaf.1 | 5xag.1 | 5xiw.1 | 5xke.1 | 5xkf.1 | 5xkg.1 | 5xkh.1 | 5xp3.1 | 5yl2.1 | 5ylj.1 | 5yls.1 | 6b0c.1 | 6b0c.2 | 6b0i.1 | 6b0i.2 | 6b0l.1 | 6b0l.2 | 6bbn.1 | 6bjc.1 | 6cvj.1 | 6cvj.2 | 6cvn.1 | 6cvn.2 | 6dpu.1 | 6dpv.1 | 6dpw.1 | 6evx.1 | 6evy.1 | 6evz.1 | 6ew0.1 | 6f7c.1 | 6fii.1 | 6fjf.1 | 6fjm.1 | 6fkj.1 | 6fkl.1 | 6gf3.1 | 6gj4.1 | 6gvm.1 | 6gvn.1 | 6gwc.1 | 6gwd.1 | 6gx7.1 | 6gx7.2 | 6hx8.1 | 6i2i.1 | 6ls4.1 | 6o2q.1 | 6o2r.1 | 6o2s.1 | 6o2s.2 | 6o2s.3 | 6o2s.4 | 6o2s.5 | 6o2s.6 | 6o2s.7 | 6o2s.8 | 6o2s.9 | 6o2s.10 | 6o2s.11 | 6o2s.12 | 6o2s.13 | 6o2s.27 | 6o2s.28 | 6o2s.29 | 6o2s.30 | 6o2s.31 | 6o2s.32 | 6o2s.33 | 6o2s.34 | 6o2s.35 | 6o2s.36 | 6o2s.37 | 6o2s.38 | 6o2s.39 | 6o2s.53 | 6o2s.54 | 6o2s.55 | 6o2s.56 | 6o2s.57 | 6o2s.58 | 6o2s.59 | 6o2s.60 | 6o2s.61 | 6o2s.62 | 6o2s.63 | 6o2s.64 | 6o2s.65 | 6o2s.79 | 6o2s.80 | 6o2s.81 | 6o2s.82 | 6o2s.83 | 6o2s.84 | 6o2s.85 | 6o2s.86 | 6o2s.87 | 6o2s.88 | 6o2s.89 | 6o2s.90 | 6o2s.91 | 6o2t.1 | 6o2t.2 | 6o2t.3 | 6o2t.4 | 6o2t.5 | 6o2t.6 | 6o2t.7 | 6o2t.8 | 6o2t.9 | 6o2t.10 | 6o2t.11 | 6o2t.12 | 6o2t.13 | 6o2t.27 | 6o2t.28 | 6o2t.29 | 6o2t.30 | 6o2t.31 | 6o2t.32 | 6o2t.33 | 6o2t.34 | 6o2t.35 | 6o2t.36 | 6o2t.37 | 6o2t.38 | 6o2t.39 | 6o2t.53 | 6o2t.54 | 6o2t.55 | 6o2t.56 | 6o2t.57 | 6o2t.58 | 6o2t.59 | 6o2t.60 | 6o2t.61 | 6o2t.62 | 6o2t.63 | 6o2t.64 | 6o2t.65 | 6o2t.79 | 6o2t.80 | 6o2t.81 | 6o2t.82 | 6o2t.83 | 6o2t.84 | 6o2t.85 | 6o2t.86 | 6o2t.87 | 6o2t.88 | 6o2t.89 | 6o2t.90 | 6o2t.91 | 6qqn.1 | 6qtn.1 | 6qus.1 | 6quy.1 | 6qve.1 | 6qvj.1 | 6s8l.1 | 6ses.1 | 6tde.1 | 6th4.1 | 6wsl.1 | 6wvl.1 | 6wvm.1 | 6wvr.1 | 6wwe.1 | 6wwf.1 | 6wwg.1 | 6wwh.1 | 6wwi.1 | 6wwj.1 | 6wwk.1 | 6wwl.1 | 6wwm.1 | 6wwn.1 | 6wwo.1 | 6wwp.1 | 6wwq.1 | 6wwr.1 | 6wws.1 | 6wwt.1 | 6wwu.1 | 6wwv.1 | 6y4m.1 | 6y4n.1 | 6y6d.1 | 6zwb.1 | 6zwc.1 | 7ac5.1 | 7alr.1 | 7au5.1 | 7cbz.1 | 7cnm.1 | 7cnn.1 | 7cno.1 | 7cpd.1 | 7cpq.1 | 7dad.1 | 7dae.1 | 7daf.1 | 7db9.1 | 7dba.1 | 7dbb.1 | 7dbc.1 | 7dbd.1 | 7dmz.1 | 7dn0.1 | 7emj.1 | 7en3.1 | 7exc.1 | 7l05.1 | 7lvq.1 | 7lvr.1 | 7lxb.1 | 7m18.1 | 7m20.1 | 7nb8.1 | 7nba.1 | 7ogn.1 | 7pjf.1 | 7pqc.1 | 7pqp.1 | 7q1e.1 | 7q1f.1 | 7q1f.2 | 7rs6.1 | 7sgs.1 | 7tqx.1 | 7tqy.1 | 7tqz.1 | 7tr0.1 | 7tr1.1 | 7tr2.1 | 7tr3.1 | 7yhn.1 | 7ysn.1 | 7yso.1 | 7ysp.1 | 7yyq.1 | 7yyv.1 | 7yyw.1 | 7yyx.1 | 7yyy.1 | 7yyz.1 | 7yz0.1 | 7yz1.1 | 7yz2.1 | 7yz3.1 | 7yz5.1 | 7yz6.1 | 7z01.1 | 7z02.1 | 7z0f.1 | 7z0g.1 | 7z0g.2 | 7z2n.1 | 7z2p.1 | 7z7d.1 | 7zcw.1 | 7zx2.1 | 7zyw.1 | 8a0l.1 | 8a9t.1 | 8a9z.1 | 8ahm.1 | 8asn.1 | 8b7a.1 | 8b7b.1 | 8b7c.1 | 8bde.1 | 8bdf.1 | 8bdg.1 | 8c0f.1 | 8c5c.1 | 8cld.1 | 8f18.1 | 8f1a.1 | 8jjb.1 | 8jjc.1 | 8rc1.1 | 8riv.1 | 8riw.1 | 8v2i.1