6s8k.1 | SWISS-MODEL Template Library

Modelling
Repository
Tools
Documentation
Log in
Create Account

SMTL ID : 6s8k.1

Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 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

31 PLIP interactions:

24 interactions with chain A, 7 interactions with chain B

Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, 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:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228
Water bridges: A:G.13, A:F.141, 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, B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

2 residues within 4Å:

Chain B: K.252
Ligands: GTP.1

No protein-ligand interaction detected (PLIP)

1 x PN6: (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione(Non-covalent)

PN6.3:

23 residues within 4Å:

Chain A: T.179
Chain B: Y.50, Q.134, N.165, F.167, E.198, Y.200, V.236, T.237, C.239, L.240, L.246, L.250, L.253, N.256, M.257, A.314, A.315, I.316, K.350, T.351, A.352, I.368

11 PLIP interactions:

10 interactions with chain B, 1 interactions with chain A

Hydrophobic interactions: B:F.167, B:Y.200, B:V.236, B:T.237, B:L.240, B:L.250, B:A.352, A:T.179
Hydrogen bonds: B:Y.200, B:V.236
Water bridges: B:A.254

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.4:

22 residues within 4Å:

Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, E.181, N.204, L.207, Y.222, L.225, N.226, V.229

26 PLIP interactions:

26 interactions with chain B

Hydrogen bonds: B:Q.11, B:Q.11, 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:V.175, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226
Water bridges: B:G.13, B:D.67, B:A.97, B:L.139, B:G.141, B:T.143, B:S.145
pi-Stacking: B:Y.222, B:Y.222

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

La Sala, G. et al., Structure, Thermodynamics, and Kinetics of Plinabulin Binding to Two Tubulin Isotypes. Chem (2019)

Release Date

2019-11-27

Peptides

Tubulin alpha-1B chain: A
Tubulin beta-2B chain: B
Designed ankyrin repeat protein (DARPIN) D1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Tubulin alpha-1B chain

Tubulin beta-2B chain

Designed ankyrin repeat protein (DARPIN) D1

Related Entries With Identical Sequence

4drx.1 | 4drx.2 | 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 | 5h74.1 | 5h7o.1 | 5ij0.1 | 5ij9.1 | 5itz.1 | 5iyz.1 | 5j2t.1 more...less...

5j2u.1 | 5jcb.1 | 5jh7.1 | 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 | 5n5n.1 | 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 | 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 | 6e7b.1 | 6e7c.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 | 6jcj.1 | 6k9v.1 | 6knz.1 | 6kpp.1 | 6lsm.1 | 6lsn.1 | 6n47.1 | 6nng.1 | 6o5m.1 | 6o5n.1 | 6o61.1 | 6ojq.1 | 6pc4.1 | 6qqn.1 | 6qtn.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 | 7en3.1 | 7jfr.1 | 7lvq.1 | 7lvr.1 | 7lz7.1 | 7lz8.1 | 7ogn.1 | 7pje.1 | 7pje.2 | 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 | 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 | 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 | 8cl9.1 | 8cla.1 | 8cld.1 | 8diq.1 | 8f18.1 | 8f1a.1 | 8huh.1 | 8riv.1 | 8riw.1

Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

Swiss Institute of BioinformaticsSIB
Schwede Group
Contact Us
Terms of use
Back to the Top