SMTL ID : 6rf2.1

Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to 13-protofilament GDP.Pi-microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, D.60, E.62, A.90, A.91, N.92, S.131, G.134, G.135, T.136, G.137, T.170, N.197, Y.215, N.219, I.222 Ligands: MG.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.90, A:A.91, A:N.92, A:S.131, A:G.134, A:G.135, A:T.136, A:G.137, A:T.170, A:E.174, A:E.174, A:N.197, A:N.219, A:N.219, A:N.219 GTP.7: 21 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, E.62, D.89, A.90, A.91, N.92, S.131, G.134, G.135, T.136, G.137, I.162, T.170, N.197, Y.215, N.219, I.222 Ligands: MG.8 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Q.11, D:A.12, D:A.90, D:A.91, D:N.92, D:S.131, D:G.134, D:G.135, D:T.136, D:G.137, D:T.170, D:T.170, D:N.197, D:Y.215, D:N.219, D:N.219

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.62 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.11, E.62 Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: D.242, E.245 Chain C: Q.11, E.69, A.97 Ligands: GDP.5 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.11, C:E.69, C:G.142 PO4.6: 7 residues within 4Å: Chain B: Q.11, E.69, A.97, T.143 Chain D: D.242, E.245 Ligands: GDP.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:T.143

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

GDP.4: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Chain D: L.239 Ligands: PO4.6 13 PLIP interactions: 13 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:N.204, B:N.204, B:N.226, B:N.226 GDP.5: 15 residues within 4Å: Chain A: L.239 Chain C: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: PO4.3 13 PLIP interactions: 13 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:G.144, C:N.204, C:N.204, C:N.226, C:N.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manka, S.W. et al., Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation. Embo Rep. (2020)

Release Date

2020-05-13

Peptides

Tubulin alpha-1B chain: AD
Tubulin beta-2B chain: BC
Neuronal migration protein doublecortin: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

D
A

B
B

C
b

E
C

Tubulin alpha-1B chain

Tubulin beta-2B chain

Neuronal migration protein doublecortin

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