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SMTL ID : 8utw.1

KIF1A[1-393] P305L mutant APO in complex with a microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1:

19 residues within 4Å:

Chain B: G.10, Q.11, A.12, Q.15, E.71, D.98, A.100, N.101, S.140, G.143, G.144, T.145, I.171, E.183, N.206, Y.224, N.228
Chain C: N.247
Ligands: MG.2

14 PLIP interactions:

13 interactions with chain B, 1 interactions with chain C

Hydrogen bonds: B:Q.11, B:Q.11, B:A.100, B:N.101, B:N.101, B:S.140, B:T.145, B:E.183, B:N.206, B:N.206, B:N.228, B:N.228
pi-Stacking: B:Y.224
Salt bridges: C:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain B: E.71, D.98
Ligands: GTP.1

2 PLIP interactions:

2 interactions with chain B

Metal complexes: B:E.71, B:D.98

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

GDP.3:

13 residues within 4Å:

Chain C: Q.11, C.12, E.69, S.138, G.140, G.141, T.143, V.169, D.177, E.181, N.204, Y.222, N.226

14 PLIP interactions:

14 interactions with chain C

Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:E.69, C:S.138, C:G.140, C:T.143, C:T.143, C:D.177, C:E.181, C:N.204, C:N.204, C:N.226, C:N.226

1 x TA1: TAXOL(Non-covalent)

TA1.4:

19 residues within 4Å:

Chain C: 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, Q.279, P.358, R.359, G.360, L.361

15 PLIP interactions:

15 interactions with chain C

Hydrophobic interactions: C:V.23, C:D.26, C:L.215, C:D.224, C:H.227, C:L.228, C:A.231, C:F.270, C:P.358
Hydrogen bonds: C:D.26, C:Q.279, C:R.359
Salt bridges: C:H.227, C:H.227
pi-Stacking: C:H.227

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Benoit, M.P.M.H. et al., Cryo-EM unveils kinesin KIF1A's processivity mechanism and the impact of its pathogenic variant P305L. Nat Commun (2024)

Release Date

2024-06-12

Peptides

Kinesin-like protein KIF1A: A
Tubulin alpha-1B chain: B
Tubulin beta-2B chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
A

C
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Kinesin-like protein KIF1A

Tubulin alpha-1B chain

Tubulin beta-2B chain

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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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Extreme

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