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SMTL ID : 7yz5.1

Molecular snapshots of drug release from tubulin: 100 milliseconds (steady state)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 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, 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:

26 interactions with chain A, 4 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: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:E.71, A:E.71, A:G.142, A:T.145, A:T.145, B:K.252, 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-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:

4 interactions with chain A, 1 Ligand-Water interactions

Metal complexes: A:D.39, A:T.41, A:T.41, A:E.55, H₂O.2

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

GDP.4:

15 residues within 4Å:

Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.175, 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:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226
Water bridges: B:G.13, B:A.97, B:G.140, B:G.140, B:G.141, B:G.141

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
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Extreme

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