SMTL ID : 3dco.1

Drosophila NOD (3DC4) and Bovine Tubulin (1JFF) Docked into the 11-Angstrom Cryo-EM Map of Nucleotide-Free NOD Complexed to the Microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 11.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.109, D.241 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.109 MG.3: 4 residues within 4Å: Chain B: Q.11, D.69, E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP)

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

ADP.2: 11 residues within 4Å: Chain A: R.29, P.32, Q.103, T.104, G.105, T.106, G.107, K.108, S.109, Y.110 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.29, A:G.105, A:T.106, A:T.106, A:G.107, A:K.108, A:S.109, A:Y.110 Salt bridges: A:K.108 pi-Stacking: A:Y.110, A:Y.110

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain B: Y.282, H.283 No protein-ligand interaction detected (PLIP)

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

GTP.5: 22 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Chain C: L.246, K.252 Ligands: MG.3 22 PLIP interactions: 20 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:G.144, B:T.145, B:T.145, B:G.146, B:T.179, B:T.179, B:E.183, B:N.206, B:N.228, 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.6: 15 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, E.181, N.204, Y.222, N.226 15 PLIP interactions: 15 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:D.177, C:D.177, C:E.181, C:N.204, C:N.226, C:N.226, C:N.226

1 x TA1: TAXOL(Non-covalent)

TA1.7: 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, P.272, L.273, T.274, S.275, R.276, P.358, R.359, G.360 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.23, C:D.26, C:L.215, C:H.227, C:L.228, C:F.270, C:F.270, C:F.270, C:P.358 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

Cochran, J.C. et al., ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement. Cell(Cambridge,Mass.) (2009)

Release Date

2009-02-10

Peptides

Kinesin-like protein Nod: A
Bovine Alpha Tubulin: B
Bovine Beta Tubulin: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
N

B
A

C
B

Kinesin-like protein Nod

Bovine Alpha Tubulin

Bovine Beta Tubulin

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