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SMTL ID : 8f1a.1

Apo KIF20A[1-565] class-1 in complex with a microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1:

22 residues within 4Å:

Chain A: G.10, Q.11, A.12, Q.15, D.69, A.99, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228
Chain B: L.246, K.252
Ligands: MG.2

19 PLIP interactions:

17 interactions with chain A, 2 interactions with chain B

Hydrogen bonds: A:Q.11, A:Q.11, A:Q.15, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, 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
pi-Cation interactions: A:Y.224
Salt bridges: B:K.252, B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain A: Q.11
Chain B: K.252
Ligands: GTP.1

No protein-ligand interaction detected (PLIP)

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

GDP.3:

14 residues within 4Å:

Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226

14 PLIP interactions:

14 interactions with chain B

Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, 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 TA1: TAXOL(Non-covalent)

TA1.4:

21 residues within 4Å:

Chain B: E.22, V.23, D.26, E.27, L.215, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, P.358, R.359, G.360, L.361

18 PLIP interactions:

18 interactions with chain B

Hydrophobic interactions: B:E.22, B:V.23, B:V.23, B:D.26, B:L.215, B:D.224, B:H.227, B:L.228, B:L.228, B:A.231, B:F.270, B:L.361
Hydrogen bonds: B:T.274, B:T.274, B:Q.279, B:R.359, B:G.360
pi-Stacking: B:H.227

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Ranaivoson, F.M. et al., Nucleotide-free structures of KIF20A illuminate atypical mechanochemistry in this kinesin-6. Open Biology (2023)

Release Date

2023-09-20

Peptides

Tubulin alpha-1B chain: A
Tubulin beta-2B chain: B
Kinesin-like protein KIF20A: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
K

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

Kinesin-like protein KIF20A

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Cartoon
Tube
Trace
Lines
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Licorice
Hyperball
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Surface
Spacefill
Outline
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Background

Transparent

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