SMTL ID : 4atu.1

Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM map of doublecortin-stabilised microtubules reconstructed in absence of kinesin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 8.30 Å

Oligo State

hetero-4-4-1-mer

Ligands

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

GDP.1: 15 residues within 4Å: Chain A: 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 A Hydrogen bonds: A:Q.11, A:C.12, A:S.138, A:G.142, A:T.143, A:T.143, A:T.143, A:T.143, A:D.177, A:E.181, A:N.204, A:N.204, A:Y.222, A:N.226, A:N.226 GDP.3: 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:C.12, C:S.138, C:G.142, C:T.143, C:T.143, C:T.143, C:T.143, C:D.177, C:E.181, C:N.204, C:N.204, C:Y.222, C:N.226, C:N.226 GDP.5: 15 residues within 4Å: Chain E: 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 E Hydrogen bonds: E:Q.11, E:C.12, E:S.138, E:G.142, E:T.143, E:T.143, E:T.143, E:T.143, E:D.177, E:E.181, E:N.204, E:N.204, E:Y.222, E:N.226, E:N.226 GDP.7: 15 residues within 4Å: Chain G: 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 G Hydrogen bonds: G:Q.11, G:C.12, G:S.138, G:G.142, G:T.143, G:T.143, G:T.143, G:T.143, G:D.177, G:E.181, G:N.204, G:N.204, G:Y.222, G:N.226, G:N.226

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

GTP.2: 21 residues within 4Å: Chain A: L.246, K.252 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 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:A.100, B:N.101, B:S.140, B:G.144, B:T.145, B:G.146, B:T.179, B:T.179, B:E.183, B:N.206, B:Y.224, B:N.228, B:N.228 pi-Stacking: B:Y.224, B:Y.224 Salt bridges: A:K.252, A:K.252 GTP.4: 21 residues within 4Å: Chain C: L.246, K.252 Chain D: 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 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, D:A.100, D:N.101, D:S.140, D:G.144, D:T.145, D:G.146, D:T.179, D:T.179, D:E.183, D:N.206, D:Y.224, D:N.228, D:N.228 pi-Stacking: D:Y.224, D:Y.224 Salt bridges: C:K.252, C:K.252 GTP.6: 21 residues within 4Å: Chain E: L.246, K.252 Chain F: 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 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:Q.11, F:Q.11, F:A.12, F:A.100, F:N.101, F:S.140, F:G.144, F:T.145, F:G.146, F:T.179, F:T.179, F:E.183, F:N.206, F:Y.224, F:N.228, F:N.228 pi-Stacking: F:Y.224, F:Y.224 Salt bridges: E:K.252, E:K.252 GTP.8: 21 residues within 4Å: Chain G: Q.245, L.246 Chain H: 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 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:Q.11, H:Q.11, H:A.12, H:A.100, H:N.101, H:S.140, H:G.144, H:T.145, H:G.146, H:T.179, H:T.179, H:E.183, H:N.206, H:Y.224, H:N.228, H:N.228 pi-Stacking: H:Y.224, H:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J.S. et al., Molecular Basis for Specific Regulation of Neuronal Kinesin- 3 Motors by Doublecortin Family Proteins. Mol.Cell (2012)

Release Date

2012-09-26

Peptides

TUBULIN BETA-2B CHAIN: ACEG
TUBULIN ALPHA-1D CHAIN: BDFH
NEURONAL MIGRATION PROTEIN DOUBLECORTIN: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

B
B

D
D

F
F

H
H

I
I

TUBULIN BETA-2B CHAIN

TUBULIN ALPHA-1D CHAIN

NEURONAL MIGRATION PROTEIN DOUBLECORTIN

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