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SMTL ID : 8ql9.1

Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution: 1 ns structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1:

24 residues within 4Å:

Chain A: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231
Ligands: MG.2

28 PLIP interactions:

28 interactions with chain A

Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, 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:Q.11, A:G.13, A:F.141, A:T.145, A:T.145, A:T.179
pi-Stacking: A:Y.224, A:Y.224

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2:

1 residues within 4Å:

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.44, G.45, E.55

5 PLIP interactions:

5 interactions with chain A

Metal complexes: A:D.39, A:T.41, A:T.41, A:G.44, 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, D.67, S.138, G.141, G.142, T.143, G.144, V.169, P.171, S.176, E.181, N.204, Y.222, N.226

19 PLIP interactions:

19 interactions with chain B

Hydrogen bonds: 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:L.139, B:G.141, B:G.141, B:T.143, B:T.143
pi-Stacking: B:Y.222, B:Y.222

1 x IBL: Azo-Combretastatin A4 (cis)(Non-covalent)

IBL.5:

21 residues within 4Å:

Chain A: T.179, A.180, V.181
Chain B: G.235, V.236, C.239, L.240, A.248, D.249, L.253, N.256, M.257, A.314, A.315, I.316, N.347, N.348, V.349, K.350, A.352, I.368

8 PLIP interactions:

1 interactions with chain A, 7 interactions with chain B

Hydrogen bonds: A:V.181, B:C.239
Hydrophobic interactions: B:A.248, B:L.253, B:N.256, B:A.314, B:K.350, B:K.350

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Weinert, T. et al., Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution. To Be Published

Release Date

2024-11-13

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

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Extreme

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