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SMTL ID : 7pjf.1

Inhibiting parasite proliferation using a rationally designed anti-tubulin agent

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1:

23 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, E.183, N.206, Y.224, N.228, I.231
Chain B: K.252
Ligands: MG.2

22 PLIP interactions:

21 interactions with chain A, 1 interactions with chain B

Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.69, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:V.177, 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.3:

22 residues within 4Å:

Chain B: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226
Ligands: MG.4

29 PLIP interactions:

29 interactions with chain B

Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:A.97, B:G.98, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226
Water bridges: B:Q.11, B:G.13, B:D.67, B:N.99, B:L.139, B:T.143, B:S.145, B:S.145, B:S.172, B:S.172
pi-Stacking: B:Y.222, B:Y.222

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2:	2 residues within 4Å: Chain A: D.69 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)
MG.4:	1 residues within 4Å: Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gaillard, N. et al., Inhibiting parasite proliferation using a rationally designed anti-tubulin agent. Embo Mol Med (2021)

Release Date

2021-09-22

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
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-3 chain

Designed ankyrin repeat protein (DARPIN) D1

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

Background

Transparent

Resolution

Low
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High
Extreme

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