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SMTL ID : 7yyz.1

Molecular snapshots of drug release from tubulin: 10 microseconds after photoactivation.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1:

25 residues within 4Å:

Chain A: G.10, Q.11, A.12, Q.15, D.69, 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 B: K.252
Ligands: MG.2

30 PLIP interactions:

28 interactions with chain A, 2 interactions with chain B

Hydrogen bonds: A:Q.11, 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:T.179, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228
Water bridges: A:G.13, A:G.142, A:T.145, A:T.145, 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:

2 residues within 4Å:

Chain A: 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.44, G.45, E.55

5 PLIP interactions:

5 interactions with chain A

Metal complexes: A:D.39, A:T.41, A:G.44, A:E.55, 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, I.16, N.99, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, N.226

20 PLIP interactions:

20 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:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226
Water bridges: B:G.13, B:N.99, B:G.141, B:T.143, B:S.145
pi-Stacking: B:Y.222, B:Y.222

1 x VYT: Azo-Combretastatin A4 (trans)(Non-covalent)

VYT.5:

19 residues within 4Å:

Chain A: T.179, A.180, V.181
Chain B: V.236, L.240, L.246, N.247, A.248, D.249, K.252, L.253, N.256, M.257, T.312, I.316, N.347, N.348, K.350, I.368

7 PLIP interactions:

7 interactions with chain B

Hydrophobic interactions: B:L.253, B:N.256, B:K.350, B:K.350
Hydrogen bonds: B:N.247, B:A.248, B:D.249

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Wranik, M. et al., Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography. Nat Commun (2023)

Release Date

2023-02-22

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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