SMTL ID : 9pnd.1

In situ microtubule of EpoB-induced regenerating axons

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.19 Å

Oligo State

hetero-2-2-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: Q.11 Ligands: GDP.2 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.10: 2 residues within 4Å: Chain D: E.71 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.71

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

GDP.2: 15 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.1 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:Q.15, A:S.138, A:G.142, A:T.143, A:T.143, A:T.143, A:G.144, A:D.177, A:N.204, A:Y.222, A:Y.222, A:N.226, A:N.226 pi-Cation interactions: A:Y.222 GDP.5: 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, N.204, Y.222, N.226 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:Y.222, B:N.226, B:N.226 pi-Cation interactions: B:Y.222

2 x EPB: 7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE(Non-covalent)

EPB.3: 12 residues within 4Å: Chain A: L.215, L.217, D.224, H.227, L.228, F.270, T.274, R.276, Q.279, R.282, L.284, L.361 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.215, A:L.215, A:L.228, A:F.270, A:T.274, A:R.282, A:L.284 Hydrogen bonds: A:D.224, A:D.224, A:R.276 EPB.6: 11 residues within 4Å: Chain B: L.215, L.217, D.224, H.227, L.228, F.270, T.274, R.276, Q.279, R.282, G.360 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.215, B:L.228, B:F.270, B:T.274, B:R.276, B:R.282 Hydrogen bonds: B:D.224

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

GTP.7: 23 residues within 4Å: Chain B: L.246, K.252 Chain C: 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, N.228 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.11, C:A.12, C:A.99, C:N.101, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:G.146, C:T.179, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.9: 19 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, Y.224, N.228, I.231 Ligands: MG.10 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:A.12, D:Q.15, D:A.99, D:N.101, D:N.101, D:S.140, D:G.143, D:G.144, D:T.145, D:T.145, D:G.146, D:N.228, D:N.228, D:N.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bodakuntla, S. et al., In situ structural mechanism of epothilone-B-induced CNS axon regeneration. Nature (2025)

Release Date

2025-11-12

Peptides

Tubulin beta-3 chain: AB
Detyrosinated tubulin alpha-1A chain: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

Tubulin beta-3 chain

Detyrosinated tubulin alpha-1A chain

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