SMTL ID : 6mzf.1 (1 other biounit)

Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with Tumor Overexpressed Gene (TOG) Domain Arrays

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 4.40 Å

Oligo State

hetero-4-4-2-4-mer

Ligands

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

GTP.1: 24 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, V.177, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, 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:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.5: 24 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, V.177, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.6 20 PLIP interactions: 1 interactions with chain D, 19 interactions with chain C Salt bridges: D:K.252 Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 GTP.9: 24 residues within 4Å: Chain H: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, V.177, E.183, N.206, Y.224, N.228, I.231 Chain I: K.252 Ligands: MG.10 18 PLIP interactions: 17 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:Q.11, H:A.12, H:A.99, H:A.100, H:N.101, H:S.140, H:G.144, H:T.145, H:G.146, H:V.177, H:E.183, H:N.206, H:N.206, H:N.228, H:N.228 pi-Stacking: H:Y.224, H:Y.224 Salt bridges: I:K.252 GTP.13: 25 residues within 4Å: Chain J: 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, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain K: K.252 Ligands: MG.14 20 PLIP interactions: 19 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:Q.11, J:A.12, J:A.99, J:A.100, J:N.101, J:S.140, J:G.144, J:T.145, J:G.146, J:V.177, J:T.179, J:E.183, J:N.206, J:N.206, J:Y.224, J:N.228, J:N.228 pi-Stacking: J:Y.224, J:Y.224 Salt bridges: K:K.252

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 3 residues within 4Å: Chain A: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.11, E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: GDP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain H: E.71 Chain I: K.252 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.71 MG.12: 3 residues within 4Å: Chain I: D.67, E.69 Ligands: GDP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain J: Q.11, E.71 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain K: Q.11 Ligands: GDP.15 No protein-ligand interaction detected (PLIP)

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

GDP.3: 16 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, Y.222, N.226 Ligands: MG.4 15 PLIP interactions: 15 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:G.144, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.7: 16 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, Y.222, N.226 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.11: 16 residues within 4Å: Chain I: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, Y.222, N.226 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:Q.11, I:C.12, I:S.138, I:G.142, I:T.143, I:T.143, I:G.144, I:E.181, I:N.204, I:N.204, I:Y.222, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222 GDP.15: 18 residues within 4Å: Chain K: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.16 17 PLIP interactions: 17 interactions with chain K Hydrogen bonds: K:Q.11, K:Q.11, K:Q.11, K:C.12, K:S.138, K:G.142, K:T.143, K:T.143, K:T.143, K:G.144, K:E.181, K:N.204, K:N.204, K:N.226, K:N.226 pi-Stacking: K:Y.222, K:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nithianantham, S. et al., Structural basis of tubulin recruitment and assembly by microtubule polymerases with Tumor Overexpressed Gene (TOG) domain arrays. Elife (2018)

Release Date

2018-11-28

Peptides

Tubulin alpha-1A chain: ACHJ
Tubulin beta chain: BDIK
Protein Stu2p/Alp14p: EL
Designed ankyrin repeat protein (DARPIN) D1: FGMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

H
H

J
J

B
B

D
D

I
I

K
K

E
E

L
L

F
F

G
G

M
M

N
N

Tubulin alpha-1A chain

Tubulin beta chain

Protein Stu2p/Alp14p

Designed ankyrin repeat protein (DARPIN) D1

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