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SMTL ID : 6s8k.1

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

Coordinates

PDB Format Compare

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

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