SMTL ID : 5syg.2 (2 other biounits)

Cryo-EM reconstruction of zampanolide-bound microtubule

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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, E.71, D.98, 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, I.231 Chain B: L.246, K.252 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:D.98, 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: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, B:K.252, B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71

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

GDP.3: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 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:G.144, B:D.177, B:D.177, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

1 x ZPN: (2Z,4E)-N-[(S)-[(1S,2E,5S,8E,10Z,17S)-3,11-dimethyl-19-methylidene-7,13-dioxo-6,21-dioxabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl](hydroxy)methyl]hexa-2,4-dienamide(Covalent)

ZPN.4: 12 residues within 4Å: Chain B: L.215, H.227, L.228, A.231, F.270, P.272, L.273, T.274, Q.279, R.282, Q.292, R.359 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.228, B:A.231, B:F.270, B:F.270, B:P.272, B:P.272, B:L.273, B:T.274, B:Q.279, B:R.359 Hydrogen bonds: B:T.274 Salt bridges: B:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kellogg, E.H. et al., Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures. J. Mol. Biol. (2017)

Release Date

2017-02-01

Peptides

Tubulin alpha chain: A
Tubulin beta chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tubulin alpha chain

Tubulin beta chain

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