SMTL ID : 4hna.1

Kinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

GTP.1: 25 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, 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:Q.11, A:A.12, 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:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: Q.11, D.67, E.69 Ligands: GDP.3, ALF.5 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain D: T.92, S.202 Ligands: ADP.6, ALF.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.92, D:S.202, H2O.1, H2O.1

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

GDP.3: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.4, ALF.5 15 PLIP interactions: 15 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:G.144, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

2 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.5: 9 residues within 4Å: Chain B: E.69, G.96, A.97, G.98, N.99, G.142, T.143 Ligands: GDP.3, MG.4 No protein-ligand interaction detected (PLIP) ALF.8: 12 residues within 4Å: Chain D: T.87, S.88, K.91, N.198, H.200, S.201, S.202, L.232, A.233, G.234 Ligands: ADP.6, MG.7 No protein-ligand interaction detected (PLIP)

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 13 residues within 4Å: Chain D: R.14, R.16, P.17, T.87, S.88, S.89, G.90, K.91, T.92, H.93, N.198 Ligands: MG.7, ALF.8 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:R.14, D:S.88, D:S.89, D:G.90, D:K.91, D:T.92, D:H.93, D:N.198 Water bridges: D:T.92, D:S.202, D:D.231 Salt bridges: D:K.91 pi-Stacking: D:H.93, D:H.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gigant, B. et al., Structure of a kinesin-tubulin complex and implications for kinesin motility. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-06-12

Peptides

Tubulin alpha chain: A
Tubulin beta chain: B
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2: 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) D2

Kinesin-1 heavy chain

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