SMTL ID : 3j6p.1

Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain B: Q.11, D.69, E.71 Ligands: GTP.2 No protein-ligand interaction detected (PLIP)

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

GTP.2: 24 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain C: L.246, K.252 Ligands: MG.1 23 PLIP interactions: 21 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:A.100, B:A.100, B:N.101, B:S.140, B:S.140, B:G.144, B:T.145, B:G.146, B:T.179, B:T.179, B:E.183, B:N.206, B:N.206, B:Y.224, B:N.228, B:N.228 pi-Stacking: B:Y.224, B:Y.224 Salt bridges: C:K.252, C:K.252

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

GDP.3: 16 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, D.177, T.178, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Q.11, C:Q.11, C:C.12, C:S.138, C:G.142, C:T.143, C:T.143, C:T.143, C:T.143, C:G.144, C:D.177, C:E.181, C:N.204, C:Y.222, C:N.226, 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, L.273, T.274, S.275, R.276, P.358, R.359, G.360, L.361 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.23, C:V.23, C:D.26, C:H.227, C:L.228, C:F.270, C:F.270, C:F.270, C:P.358, C:L.361 Hydrogen bonds: C:T.274, C:P.358, C:G.360 pi-Stacking: C:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Uchimura, S. et al., A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. J.Cell Biol. (2015)

Release Date

2014-12-31

Peptides

Dynein heavy chain, cytoplasmic: A
Tubulin alpha-1A chain: B
Tubulin beta chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

Dynein heavy chain, cytoplasmic

Tubulin alpha-1A chain

Tubulin beta chain

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