SMTL ID : 7x4n.1

Crystal Structure of C. elegans kinesin-4 KLP-12 complexed with tubulin and DARPin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, E.71, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, P.173, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:D.98, A:A.99, A:A.99, A:N.101, A:S.140, A:G.144, 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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.69, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.5: 6 residues within 4Å: Chain D: K.90, T.91, S.217, D.261, L.262 Ligands: ANP.4 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.91, D:S.217

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

GDP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:T.143, B:G.144, 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 ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.4: 16 residues within 4Å: Chain D: R.11, R.13, P.14, Q.85, T.86, G.87, S.88, G.89, K.90, T.91, H.92, N.213, S.216, S.217, G.264 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.11, D:G.87, D:S.88, D:G.89, D:K.90, D:K.90, D:K.90, D:T.91, D:H.92, D:N.213, D:S.217, D:G.264 pi-Stacking: D:H.92, D:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taguchi, S. et al., Structural model of microtubule dynamics inhibition by kinesin-4 from the crystal structure of KLP-12 -tubulin complex. Elife (2022)

Release Date

2022-09-21

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
E

Tubulin alpha-1A chain

Tubulin beta chain

DARPin

Kinesin-like protein

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