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SMTL ID : 7tr3.1

CaKip3[2-482] - AMP-PNP in complex with a dolastatin-10-stabilized tubulin ring

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:

21 residues within 4Å:

Chain A: G.10, Q.11, A.12, Q.15, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, I.171, T.179, E.183, N.206, Y.224, N.228, I.231
Ligands: MG.2

15 PLIP interactions:

15 interactions with chain A

Hydrogen bonds: A:Q.11, A:A.12, A:E.71, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.179, A:E.183, A:N.206, A:N.228
pi-Stacking: A:Y.224

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

2 residues within 4Å:

Chain A: E.71
Ligands: GTP.1

2 PLIP interactions:

2 interactions with chain A

Metal complexes: A:E.71, A:E.71

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

GDP.3:

13 residues within 4Å:

Chain B: Q.11, C.12, E.69, G.98, G.141, T.143, V.169, P.171, S.176, E.181, N.204, Y.222, N.226

15 PLIP interactions:

15 interactions with chain B

Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:E.69, B:G.96, B:G.141, B:T.143, B:T.143, B:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226
pi-Cation interactions: B:Y.222

1 x SR6: dolastatin-10(Non-covalent)

SR6.4:

9 residues within 4Å:

Chain B: Q.11, Q.15, K.174, V.175, Y.208, P.220, T.221, Y.222, G.223

4 PLIP interactions:

4 interactions with chain B

Hydrophobic interactions: B:Y.208, B:Y.222, B:Y.222
Hydrogen bonds: B:Y.222

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5:

13 residues within 4Å:

Chain C: R.32, R.34, P.35, T.188, G.189, C.190, G.191, K.192, T.193, H.194, T.300, S.301, S.302

13 PLIP interactions:

13 interactions with chain C

Hydrogen bonds: C:R.32, C:G.189, C:G.191, C:K.192, C:K.192, C:T.193, C:H.194, C:H.194, C:T.300, C:T.300, C:S.302, C:S.302
pi-Cation interactions: C:H.194

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hunter, B. et al., Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape. Nat Commun (2022)

Release Date

2022-07-20

Peptides

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

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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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