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SMTL ID : 6b0i.1 (1 other biounit)

Apo KLP10A in complex with a microtubule

Coordinates

PDB Format

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.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228
Chain C: L.246, K.252
Ligands: MG.2

24 PLIP interactions:

21 interactions with chain A, 3 interactions with chain C

Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, 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:T.179, A:T.179, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228
pi-Stacking: A:Y.224
pi-Cation interactions: A:Y.224
Salt bridges: C:K.252, C:K.252, C:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain A: Q.11, D.98
Chain C: K.252
Ligands: GTP.1

No protein-ligand interaction detected (PLIP)

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

GDP.3:

15 residues within 4Å:

Chain C: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226

16 PLIP interactions:

16 interactions with chain C

Hydrogen bonds: C:Q.11, C:C.12, C:S.138, C:G.142, C:T.143, C:G.144, C:D.177, C:E.181, C:N.204, C:N.204, C:Y.222, C:N.226, C:N.226
pi-Stacking: C:Y.222, C:Y.222
pi-Cation interactions: C:Y.222

1 x TA1: TAXOL(Non-covalent)

TA1.4:

16 residues within 4Å:

Chain C: V.23, D.26, L.215, D.224, H.227, L.228, A.231, S.234, P.272, L.273, T.274, R.276, P.358, R.359, G.360, L.361

13 PLIP interactions:

13 interactions with chain C

Hydrophobic interactions: C:V.23, C:D.26, C:H.227, C:L.228, C:A.231, C:R.276, C:L.361
Hydrogen bonds: C:T.274, C:R.359, C:G.360
Salt bridges: C:H.227, C:R.276
pi-Cation interactions: C:H.227

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Benoit, M.P.M.H. et al., Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s. Nat Commun (2018)

Release Date

2018-05-02

Peptides

Tubulin alpha-1B chain: A
Kinesin-like protein Klp10A: B
Tubulin beta chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
K

C
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Tubulin alpha-1B chain

Kinesin-like protein Klp10A

Tubulin beta chain

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

Background

Transparent

Resolution

Low
Medium
High
Extreme

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