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SMTL ID : 7z01.1

Z-SBTubA4 photoswitch bound to tubulin-DARPin D1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1:

26 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.142, 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

28 PLIP interactions:

25 interactions with chain A, 3 interactions with chain B

Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:A.100, A:N.101, 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:S.140, A:G.142, A:T.145, A:T.145, B:K.252, B:K.252
pi-Stacking: A:Y.224, A:Y.224
Salt bridges: B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

3 residues within 4Å:

Chain A: Q.11, E.71
Ligands: GTP.1

No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3:

5 residues within 4Å:

Chain A: D.39, T.41, G.45, D.47, E.55

4 PLIP interactions:

4 interactions with chain A

Metal complexes: A:T.41, A:G.45, A:D.47, A:E.55

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

GDP.4:

17 residues within 4Å:

Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, G.141, G.142, T.143, G.144, P.171, V.175, E.181, N.204, Y.222, N.226

16 PLIP interactions:

16 interactions with chain B

Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:G.144, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226
Water bridges: B:N.99, B:S.138, B:G.140
pi-Stacking: B:Y.222, B:Y.222

1 x I8R: 2-methoxy-5-[2-(5,6,7-trimethoxy-1,3-benzothiazol-2-yl)ethyl]phenol(Non-covalent)

I8R.5:

26 residues within 4Å:

Chain A: T.179, A.180, V.181
Chain B: G.235, V.236, T.237, C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, T.312, V.313, A.314, A.315, I.316, N.347, N.348, V.349, K.350, T.351, A.352, I.368

4 PLIP interactions:

4 interactions with chain B

Hydrophobic interactions: B:A.248, B:L.253, B:N.256, B:K.350

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gao, L. et al., In Vivo Photocontrol of Microtubule Dynamics and Integrity, Migration and Mitosis, by the Potent GFP-Imaging-Compatible Photoswitchable Reagents SBTubA4P and SBTub2M. J.Am.Chem.Soc. (2022)

Release Date

2022-03-30

Peptides

Tubulin alpha-1B chain: A
Tubulin beta-2B chain: B
Designed Ankyrin Repeat Protein (DARPIN) D1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Tubulin alpha-1B chain

Tubulin beta-2B chain

Designed Ankyrin Repeat Protein (DARPIN) D1

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
Medium
High
Extreme

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