SMTL ID : 8cl9.1

Tubulin-DARPin D1 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 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.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: Q.245, 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:D.69, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228, B:Q.245 Water bridges: A:G.13, A:L.70, A:S.140, A:F.141, A:G.142, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.3: 24 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, D.67, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, S.176, E.181, N.204, L.207, Y.222, N.226 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:D.67, B:A.97, B:G.98, B:N.99, 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:G.140, B:G.141, B:S.145 pi-Stacking: B:Y.222, B:Y.222

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69, E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP)

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. Nat Commun (2023)

Release Date

2023-12-13

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

Tubulin alpha-1B chain

Tubulin beta-2B chain

DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D1

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