SMTL ID : 5eyp.1

TUBULIN-DARPIN COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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, S.178, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 27 PLIP interactions: 24 interactions with chain A, 3 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:T.145, A:G.146, A:S.178, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:D.98, A:F.141, 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)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 Ligands: GOL.5 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:K.394 Hydrogen bonds: B:N.347 Water bridges: B:N.347 SO4.4: 5 residues within 4Å: Chain A: V.177, S.178, P.222, Y.224, L.227 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.178 Water bridges: A:S.178, A:Y.224, A:Y.224 SO4.10: 3 residues within 4Å: Chain B: T.221, G.223, R.276 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.221, B:T.221 Water bridges: B:G.223, B:G.223, B:R.276, B:R.276 Salt bridges: B:R.276

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Y.172, P.173, P.175, R.390, K.394 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.394 GOL.6: 4 residues within 4Å: Chain A: R.402, H.406, V.409, E.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.415 Water bridges: A:V.405, A:H.406 GOL.7: 4 residues within 4Å: Chain A: Q.15, N.18, T.225, N.228 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.18, A:T.225, A:T.225, A:N.228 Water bridges: A:Q.15, A:E.77, A:T.225 GOL.11: 5 residues within 4Å: Chain B: N.52, R.86, K.122, E.123, S.126 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.52, B:R.86 Water bridges: B:N.52, B:E.53, B:R.86, B:N.89, B:K.122 GOL.12: 7 residues within 4Å: Chain B: F.394, L.395, H.396, W.397 Chain C: R.23, Y.57 Ligands: GOL.13 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:H.396, B:W.397, C:R.23, C:Y.57 Water bridges: B:L.395, B:H.396 GOL.13: 9 residues within 4Å: Chain B: R.391, K.392, A.393, H.396 Chain C: R.23, L.48, T.56, Y.57 Ligands: GOL.12 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Water bridges: B:H.396, C:S.46, C:S.46 Hydrogen bonds: C:R.23, C:R.23, C:Y.57, C:Y.57 GOL.14: 5 residues within 4Å: Chain C: T.43, D.44, A.45, G.47, L.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.45 GOL.15: 4 residues within 4Å: Chain B: V.179 Chain C: I.90, G.91, H.92 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.90, C:G.91 Water bridges: C:H.92

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

GDP.8: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, L.207, Y.222, N.226 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:A.97, B:S.138, B:G.140, B:G.141, B:T.143, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222

1 x LOC: N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide(Non-covalent)

LOC.9: 20 residues within 4Å: Chain A: S.178, T.179, A.180, V.181 Chain B: C.239, L.240, L.246, A.248, K.252, L.253, N.256, M.257, T.312, V.313, A.314, I.316, N.348, K.350, A.352, I.368 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.246, B:A.248, B:K.252, B:L.253, B:N.256, B:K.350, B:K.350 Water bridges: B:C.239, B:L.240 Hydrogen bonds: A:V.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, S. et al., Destabilizing an interacting motif strengthens the association of a designed ankyrin repeat protein with tubulin. Sci Rep (2016)

Release Date

2016-07-20

Peptides

Tubulin alpha chain: A
Tubulin beta chain: B
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN): C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

Tubulin alpha chain

Tubulin beta chain

DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN)

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