- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.89 Å
- Oligo State
- hetero-2-2-1-1-mer
- Ligands
- 3 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)
GTP.1: 26 residues within 4Å:- Chain A: G.10, Q.11, A.12, Q.15, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231
- Chain B: K.252
- Ligands: MG.2, WIW.8
20 PLIP interactions:19 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228
- pi-Stacking: A:Y.224, A:Y.224
- Salt bridges: B:K.252
GTP.10: 25 residues within 4Å:- Chain C: G.10, Q.11, A.12, Q.15, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231
- Chain D: K.252
- Ligands: MG.11
20 PLIP interactions:19 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228
- pi-Stacking: C:Y.224, C:Y.224
- Salt bridges: D:K.252
GTP.17: 20 residues within 4Å:- Chain D: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.176, E.181, N.204, Y.222, N.226
- Ligands: MG.18
20 PLIP interactions:20 interactions with chain D- Hydrogen bonds: D:Q.11, D:C.12, D:E.69, D:A.97, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226
- pi-Stacking: D:Y.222, D:Y.222
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 3 residues within 4Å:- Chain A: D.69, E.71
- Ligands: GTP.1
No protein-ligand interaction detected (PLIP)MG.6: 3 residues within 4Å:- Chain B: Q.11, D.177
- Ligands: GDP.5
No protein-ligand interaction detected (PLIP)MG.11: 3 residues within 4Å:- Chain C: Q.11, E.71
- Ligands: GTP.10
No protein-ligand interaction detected (PLIP)MG.18: 2 residues within 4Å:- Chain D: Q.11
- Ligands: GTP.17
No protein-ligand interaction detected (PLIP)- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 1 residues within 4Å:- Chain A: L.117
No protein-ligand interaction detected (PLIP)EDO.9: 4 residues within 4Å:- Chain B: V.193, E.194, P.261
- Ligands: MES.7
No protein-ligand interaction detected (PLIP)EDO.13: 4 residues within 4Å:- Chain C: L.248, P.325, V.353, G.354
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:L.248
EDO.14: 3 residues within 4Å:- Chain C: I.332, G.350, F.351
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:F.351
EDO.15: 2 residues within 4Å:- Chain C: V.177, Y.224
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Y.224
EDO.16: 1 residues within 4Å:- Chain C: Y.357
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:Y.357
EDO.19: 3 residues within 4Å:- Chain C: H.393, L.397
- Chain D: D.431
No protein-ligand interaction detected (PLIP)EDO.20: 3 residues within 4Å:- Chain D: A.110, D.114
- Chain E: R.129
3 PLIP interactions:1 interactions with chain D, 2 interactions with chain E- Hydrogen bonds: D:D.114, E:R.129, E:R.129
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.4: 7 residues within 4Å:- Chain A: H.107, Y.108, E.155, H.192, T.193, E.417, E.420
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.107, A:H.192
- 1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
GDP.5: 18 residues within 4Å:- Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226
- Ligands: MG.6
17 PLIP interactions:17 interactions with chain B- Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226
- pi-Stacking: B:Y.222, B:Y.222
- 1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.7: 11 residues within 4Å:- Chain B: R.156, P.160, D.161, R.162, M.164, E.194, N.195, T.196, D.197, R.251
- Ligands: EDO.9
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:R.156
- Salt bridges: B:D.197, B:R.251
- 1 x WIW: (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one(Non-covalent)
WIW.8: 27 residues within 4Å:- Chain A: N.101, S.178, T.179, A.180, E.183
- Chain B: V.236, C.239, L.240, L.246, N.247, A.248, D.249, K.252, L.253, N.256, M.257, T.312, V.313, A.314, A.315, I.316, N.348, K.350, T.351, A.352, I.368
- Ligands: GTP.1
7 PLIP interactions:5 interactions with chain B, 2 interactions with chain A- Hydrophobic interactions: B:L.253, B:N.256, B:A.314, B:K.350
- Hydrogen bonds: B:D.249, A:T.179, A:E.183
- 1 x CA: CALCIUM ION(Non-covalent)
CA.12: 4 residues within 4Å:- Chain C: D.39, T.41, G.44, E.55
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.39, C:T.41, C:G.44, C:E.55, C:E.55
- 1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)
ACP.21: 18 residues within 4Å:- Chain F: I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333
9 PLIP interactions:9 interactions with chain F- Hydrogen bonds: F:Q.183, F:L.186, F:K.198, F:D.200, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Zhao, W., Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents. To Be Published
- Release Date
- 2024-10-09
- Peptides
- Detyrosinated tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Tubulin--tyrosine ligase: F - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CB
BD
DE
EF
F
SMTL ID : 8wmo.1
Crystal structure analysis of tubulin and heterocyclic podophyllotoxins complex for anticancer agents
Detyrosinated tubulin alpha-1B chain
Tubulin beta chain
Stathmin-4
Tubulin--tyrosine ligase
Related Entries With Identical Sequence
4i4t.1 | 4i50.1 | 4i55.1 | 4ihj.1 | 4iij.1 | 4o2a.1 | 4o2b.1 | 4o4h.1 | 4o4i.1 | 4o4j.1 | 4o4l.1 | 4tuy.1 | 4tv8.1 | 4tv9.1 | 4yj2.1 | 4yj3.1 | 5c8y.1 | 5ca0.1 | 5cb4.1 | 5eyp.1 | 5ezy.1 | 5gon.1 | 5h74.1 | 5h7o.1 | 5itz.1 | 5iyz.1 | 5j2t.1 | 5j2u.1 | 5jcb.1 | 5jh7.1 more...less...5jvd.1 | 5la6.1 | 5lov.1 | 5lp6.1 | 5lxs.1 | 5lxt.1 | 5lyj.1 | 5m7e.1 | 5m7g.1 | 5m8d.1 | 5m8g.1 | 5mf4.1 | 5mio.2 | 5nfz.1 | 5ng1.1 | 5njh.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 | 5xhc.1 | 5xi5.1 | 5xi7.1 | 5xiw.1 | 5xkf.1 | 5xkg.1 | 5xlt.1 | 5xlz.1 | 5yl2.1 | 5yl4.1 | 5ylj.1 | 5yls.1 | 5yz3.1 | 5z4p.1 | 6agk.1 | 6b0c.1 | 6b0c.2 | 6b0i.1 | 6b0i.2 | 6b0l.1 | 6b0l.2 | 6bbn.1 | 6br1.1 | 6brf.1 | 6bry.1 | 6bs2.1 | 6d88.1 | 6eg5.1 | 6f7c.1 | 6fii.1 | 6fjf.1 | 6fjm.1 | 6fkj.1 | 6fkl.1 | 6gf3.1 | 6gj4.1 | 6gvm.1 | 6gvn.2 | 6gwc.1 | 6gwd.1 | 6gx7.1 | 6gx7.2 | 6gze.1 | 6hx8.1 | 6i5c.1 | 6jcj.1 | 6k9v.1 | 6knz.1 | 6kpp.1 | 6lsm.1 | 6lsn.1 | 6n47.1 | 6nng.1 | 6o5m.1 | 6o5n.1 | 6o61.1 | 6pc4.1 | 6qqn.1 | 6qtn.1 | 6s8k.1 | 6s9e.1 | 6ses.1 | 6tde.1 | 6th4.1 | 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 | 6x1c.1 | 6x1e.1 | 6x1f.1 | 6y6d.1 | 6zwb.1 | 6zwc.1 | 7ac5.1 | 7au5.1 | 7cda.1 | 7ce6.1 | 7ce8.1 | 7cek.1 | 7cld.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 | 7dp8.1 | 7e4p.1 | 7e4q.1 | 7e4r.1 | 7e4y.1 | 7e4z.1 | 7en3.1 | 7jfr.1 | 7lvq.1 | 7lvr.1 | 7lz7.1 | 7lz8.1 | 7ogn.1 | 7q1e.1 | 7q1f.1 | 7q1f.2 | 7tqx.1 | 7tqy.1 | 7tqz.1 | 7tr0.1 | 7tr1.1 | 7tr2.1 | 7tr3.1 | 7vmg.1 | 7vmj.1 | 7vmk.1 | 7xqx.1 | 7xqy.1 | 7xr0.1 | 7xr1.1 | 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 | 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 | 8cgz.1 | 8clb.1 | 8clc.1 | 8cld.1 | 8cle.1 | 8clf.1 | 8clg.1 | 8clh.1 | 8diq.1 | 8f18.1 | 8f1a.1 | 8huh.1 | 8qea.1 | 8ql2.1 | 8ql3.1 | 8ql4.1 | 8ql5.1 | 8ql6.1 | 8ql7.1 | 8ql8.1 | 8ql9.1 | 8qla.1 | 8qlb.1 | 8r67.1 | 8riv.1 | 8riw.1 | 8utn.1 | 8uto.1 | 8utp.1 | 8utq.1 | 8utr.1 | 8uts.1 | 8utt.1 | 8utu.1 | 8utv.1 | 8utw.1 | 8uty.1 | 8wd0.1 | 8wmu.1 | 8ytx.1 | 8yu9.1 | 8yua.1 | 8zb8.1 | 9f07.1 | 9f8g.1 | 9fyd.1