SMTL ID : 6wvr.1

Tubulin dimers from a 13-protofilament, Taxol stabilized microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

GTP.1: 27 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, N.102, 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 B: L.246, K.252 Ligands: MG.2 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.15, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:T.179, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.5: 27 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, N.102, 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 D: L.246, K.252 Ligands: MG.6 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.15, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:T.179, C:E.183, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228, C:N.228 pi-Stacking: C:Y.224 Salt bridges: D:K.252, D:K.252, D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.11, D.69, T.145 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: Q.11, D.69, T.145 Chain D: K.252 Ligands: GTP.5 No protein-ligand interaction detected (PLIP)

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

GDP.3: 22 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, D.177, E.181, N.204, L.207, Y.222, L.225, N.226 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:Q.15, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.7: 23 residues within 4Å: Chain A: L.248 Chain D: G.10, Q.11, C.12, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, D.177, E.181, N.204, L.207, Y.222, L.225, N.226 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:Q.15, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:T.143, D:G.144, D:D.177, D:D.177, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

2 x TA1: TAXOL(Non-covalent)

TA1.4: 25 residues within 4Å: Chain B: K.19, E.22, V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, G.235, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:E.22, B:V.23, B:V.23, B:D.26, B:E.27, B:L.215, B:H.227, B:L.228, B:A.231, B:F.270, B:F.270, B:R.276, B:P.358, B:L.361 Hydrogen bonds: B:H.227, B:T.274, B:T.274, B:R.359 Salt bridges: B:H.227, B:R.276 pi-Stacking: B:H.227 TA1.8: 25 residues within 4Å: Chain D: K.19, E.22, V.23, D.26, E.27, L.215, L.217, D.224, H.227, L.228, A.231, S.234, G.235, F.270, P.272, L.273, T.274, S.275, R.276, Q.279, R.318, P.358, R.359, G.360, L.361 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:E.22, D:V.23, D:V.23, D:D.26, D:E.27, D:L.215, D:H.227, D:L.228, D:A.231, D:F.270, D:F.270, D:R.276, D:P.358, D:L.361 Hydrogen bonds: D:H.227, D:T.274, D:T.274, D:R.359 Salt bridges: D:H.227, D:R.276 pi-Stacking: D:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Debs, G.E. et al., Dynamic and asymmetric fluctuations in the microtubule wall captured by high-resolution cryoelectron microscopy. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-05-20

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Tubulin alpha-1B chain

Tubulin beta chain

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