SMTL ID : 4lnu.1

Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 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, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 34 PLIP interactions: 29 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, 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 Water bridges: A:G.13, A:D.98, A:D.98, A:D.98, A:F.141, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 5 residues within 4Å: Chain A: V.177, R.221, T.223, Y.224 Chain B: Q.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.223, A:Y.224 Water bridges: A:Y.224 Salt bridges: A:R.221 SO4.4: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.394 Hydrogen bonds: B:N.347 SO4.5: 4 residues within 4Å: Chain A: R.79, P.89, E.90, L.92 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.79, A:R.79, A:R.79, A:R.79, A:E.90, A:L.92, A:R.121 SO4.10: 4 residues within 4Å: Chain B: H.190, Q.191, E.194, N.195 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.191, B:N.195 Salt bridges: B:H.190 SO4.11: 3 residues within 4Å: Chain B: T.221, G.223, R.276 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.221, B:G.223 Water bridges: B:T.221, B:T.221 Salt bridges: B:R.276 SO4.12: 2 residues within 4Å: Chain B: R.390 Chain C: W.112 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Water bridges: D:K.159, D:K.159, D:R.161, B:R.390, B:R.390 Salt bridges: B:R.390 SO4.13: 5 residues within 4Å: Chain B: H.105, Y.106, L.150, S.153, Q.191 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.106, B:S.153, B:Q.191, B:Q.191 Salt bridges: B:H.105 SO4.14: 7 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, P.305, R.306 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.296 Salt bridges: B:R.306 SO4.15: 4 residues within 4Å: Chain B: G.98, N.100, K.103, W.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.100 Salt bridges: B:K.103 SO4.18: 6 residues within 4Å: Chain D: T.87, S.88, S.89, G.90, K.91, T.92 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.88, D:G.90, D:K.91, D:T.92, D:T.92 SO4.19: 4 residues within 4Å: Chain B: E.194 Chain D: R.278, S.280, K.281 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.278 Water bridges: D:R.278

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

GDP.6: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226 Water bridges: B:G.13, B:A.97, B:L.139, B:G.141, B:S.145, B:S.176 pi-Stacking: B:Y.222, B:Y.222

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 9 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, N.195, D.197, R.251 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:R.105, A:R.105 Salt bridges: B:D.197, B:R.251

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 8 residues within 4Å: Chain B: F.294, R.306, Y.310, I.333, N.337, Y.340, F.341 Ligands: SO4.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.294 GOL.9: 6 residues within 4Å: Chain B: N.52, R.86, N.89, K.122, E.123, S.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.89, B:K.122, B:S.126 Water bridges: B:N.52 GOL.16: 5 residues within 4Å: Chain B: R.391, K.392 Chain C: R.23, L.48, Y.57 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.23, C:R.23, C:Y.57 Water bridges: C:R.23, C:R.23 GOL.17: 6 residues within 4Å: Chain A: H.406, V.409 Chain D: K.256, S.259, N.263, D.279 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:S.259, D:N.263, D:D.279 Water bridges: D:K.256, A:H.406

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, L. et al., The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement. Nat Commun (2014)

Release Date

2014-12-03

Peptides

Tubulin alpha chain: A
Tubulin beta chain: B
Designed ankyrin repeat protein (DARPIN) D1: C
Kinesin-1 heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
K

Tubulin alpha chain

Tubulin beta chain

Designed ankyrin repeat protein (DARPIN) D1

Kinesin-1 heavy chain

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