SMTL ID : 9f07.1

TUBULIN:STATHMIN:DARPIN:TAU MTBR3 COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

GTP.1: 25 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 30 PLIP interactions: 27 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:L.70, A:E.71, A:N.101, A:F.141, A:T.145, A:T.179, A:T.179, A:E.183, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.13: 25 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, V.177, T.179, E.183, N.206, Y.224, N.228, I.231 Chain F: K.252 Ligands: MG.14 27 PLIP interactions: 23 interactions with chain E, 4 interactions with chain F Hydrogen bonds: E:Q.11, E:Q.11, E:A.12, E:Q.15, E:A.99, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:G.146, E:V.177, E:E.183, E:N.206, E:N.206, E:Y.224, E:N.228, E:N.228 Water bridges: E:G.13, E:D.98, E:F.141, F:K.252, F:K.252, F:K.252 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: F:K.252

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

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: GTP.13 No protein-ligand interaction detected (PLIP)

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

GDP.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 23 PLIP interactions: 23 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 Water bridges: B:D.67, B:G.98, B:S.138, B:G.140, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.15: 17 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 23 PLIP interactions: 23 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:E.181, F:N.204, F:N.204, F:Y.222, F:N.226, F:N.226 Water bridges: F:Q.11, F:G.13, F:G.98, F:G.140, F:G.141, F:T.143, F:S.145 pi-Stacking: F:Y.222, F:Y.222

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain B: R.306, H.307, G.308, R.309, S.339, Y.340, Q.426 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.307, B:R.309, B:S.339, B:Q.426 GOL.5: 5 residues within 4Å: Chain B: N.52, R.86, K.122, E.123, S.126 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.86, B:K.122, B:S.126 Water bridges: B:R.62 GOL.6: 5 residues within 4Å: Chain B: V.175, P.220, T.221, Y.222, L.225 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.222 GOL.7: 6 residues within 4Å: Chain B: D.26, E.27, Q.43, I.356, P.357, R.359 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.43, B:P.357, B:R.359 GOL.16: 4 residues within 4Å: Chain F: E.376, K.379, R.380, E.383 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.383 GOL.17: 7 residues within 4Å: Chain F: R.306, H.307, G.308, R.309, S.339, Y.340, Q.426 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.307, F:R.309, F:S.339, F:Q.426 GOL.18: 7 residues within 4Å: Chain F: R.156, P.160, D.161, R.162, D.197, R.251 Chain G: F.63 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:R.156, F:R.156, F:D.197, F:R.251, F:R.251 Water bridges: E:R.105

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 7 residues within 4Å: Chain B: F.294, D.295, S.296, R.306, N.337, Y.340, F.341 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.296, B:S.296, B:R.306 Water bridges: B:S.296 PEG.21: 5 residues within 4Å: Chain F: F.294, D.295, S.296, R.306, N.337 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.296, F:S.296 Water bridges: F:R.306

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.9: 9 residues within 4Å: Chain B: T.107, A.110, E.111, V.113, D.114, L.150 Chain C: D.74, A.77, R.81 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.74, B:E.111

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.10: 16 residues within 4Å: Chain B: G.98, N.99, D.177, V.179, V.180, F.394, W.397 Chain D: K.48, D.81, L.86, L.89, Y.90, Y.112, F.114, L.119, D.122 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:Y.90, B:N.99 Water bridges: D:K.48

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.11: 4 residues within 4Å: Chain B: F.90, V.91, F.92, L.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.92, B:Q.94 PGE.12: 10 residues within 4Å: Chain B: V.179, A.387, M.388, R.391, A.393, F.394 Chain D: L.89, Y.90, A.123, H.125 No protein-ligand interaction detected (PLIP) PGE.19: 9 residues within 4Å: Chain F: G.98, V.179, V.180, F.394, W.397 Chain H: D.81, L.89, D.110, Y.112 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:G.98, H:D.81 PGE.20: 7 residues within 4Å: Chain F: N.52, R.86, N.89, V.119, K.122, E.123, S.126 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:N.52, F:R.86, F:V.119, F:S.126 Water bridges: F:R.62 PGE.22: 9 residues within 4Å: Chain F: V.179, A.387, M.388, R.391, F.394 Chain H: L.89, Y.90, A.123, H.125 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khodja, L.A. et al., The structure of a Tau fragment bound to tubulin prompts new hypotheses on Tau mechanism and oligomerization. Pnas Nexus (2024)

Release Date

2024-11-13

Peptides

Tubulin alpha chain: AE
Tubulin beta chain: BF
Stathmin-4: CG
D2-R3: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

F
F

C
C

G
G

D
D

H
H

Tubulin alpha chain

Tubulin beta chain

Stathmin-4

D2-R3

Related Entries With Identical Sequence