SMTL ID : 8cla.1

Z-SBTubA4 photoswitch bound to tubulin-DARPin D1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GTP.1: 30 residues within 4Å: Chain A: G.9, Q.10, A.11, Q.14, I.15, D.68, D.97, A.98, A.99, N.100, N.101, S.139, G.141, G.142, G.143, T.144, G.145, I.170, P.172, V.176, S.177, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Chain B: K.252 Ligands: MG.2 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.10, A:Q.10, A:A.11, A:Q.14, A:D.68, A:A.98, A:A.99, A:N.100, A:N.100, A:S.139, A:G.143, A:T.144, A:T.144, A:G.145, A:E.182, A:N.205, A:N.205, A:Y.223, A:N.227, A:N.227 Water bridges: A:G.12, A:F.140, B:K.252, B:K.252 pi-Stacking: A:Y.223, A:Y.223 Salt bridges: B:K.252, B:K.252

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.10, E.70, D.97 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.38, T.40, G.43, G.44, F.48, N.49, E.54, H.60 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.40, A:T.40, A:G.43, A:E.54, H2O.1

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

GDP.4: 26 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, I.16, D.67, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 24 PLIP interactions: 24 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:Y.222, B:N.226, B:N.226 Water bridges: B:S.138, B:L.139, B:G.141, B:T.143, B:T.143, B:S.145, B:S.176, B:E.181 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: 29 residues within 4Å: Chain A: T.178, A.179, V.180 Chain B: Y.200, G.235, V.236, T.237, T.238, C.239, L.240, L.246, A.248, D.249, 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.367 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.248, B:L.253, B:N.256, B:K.350, B:K.350 Water bridges: B:N.347, B:V.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wranik, M. et al., A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free electron lasers. To Be Published

Release Date

2024-02-28

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

Tubulin alpha-1B chain

Tubulin beta-2B chain

Designed Ankyrin Repeat Protein (DARPIN) D1

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