SMTL ID : 7alr.1

Crystal structure of TD1-gatorbulin1 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x GLY: GLYCINE(Non-covalent)

GLY.1: 6 residues within 4Å: Chain A: K.311, T.382, Y.432, E.433, E.434, V.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.311, A:Y.432

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

GTP.2: 29 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.142, G.143, G.144, T.145, G.146, I.171, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.3 27 PLIP interactions: 23 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.69, A:A.99, A:A.100, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:G.13, A:N.101, A:N.101, 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-covalent)

MG.3: 6 residues within 4Å: Chain A: Q.11, D.69, E.71, D.98 Chain B: K.252 Ligands: GTP.2 No protein-ligand interaction detected (PLIP)

1 x RQK: (2~{R})-2-oxidanyl-2-[(6~{S},9~{S},12~{S},15~{S},17~{S})-6,10,12,17-tetramethyl-3-methylidene-7-oxidanyl-2,5,8,11,14-pentakis(oxidanylidene)-13-oxa-1,4,7,10-tetrazabicyclo[13.3.0]octadecan-9-yl]ethanamide(Non-covalent)

RQK.4: 21 residues within 4Å: Chain A: P.175, Q.176, V.177, S.178, T.179, Y.210, R.221, P.222, T.223, Y.224, L.227 Chain B: Q.245, L.246, M.323, V.326, D.327, V.349, K.350, V.351, A.352, V.353 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.179, A:Y.224, A:Y.224, A:L.227, B:V.353 Hydrogen bonds: A:P.175, A:S.178, A:S.178, A:R.221, B:D.327, B:V.351, B:V.351 Water bridges: A:R.221, B:D.327, B:D.327, B:K.350

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

SO4.5: 3 residues within 4Å: Chain A: P.175, K.394 Chain B: N.347 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.347 Water bridges: A:K.394 Salt bridges: A:K.394 SO4.6: 6 residues within 4Å: Chain A: N.18, A.19, E.22, Y.83, T.225, R.229 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.18 Salt bridges: A:R.229

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

GDP.7: 27 residues within 4Å: Chain B: G.10, Q.11, C.12, G.13, Q.15, I.16, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 25 PLIP interactions: 25 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:D.67, B:A.97, B:S.138, B:L.139, B:G.141, B:T.143, B:S.145, B:S.176, B:E.181 pi-Stacking: B:Y.222, B:Y.222

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 4 residues within 4Å: Chain B: T.386, R.390 Chain C: M.90, W.123 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:W.123, B:R.390, B:R.390 GOL.9: 8 residues within 4Å: Chain B: E.205, A.206, D.209, I.210, A.296, K.297, M.299, A.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.209, B:M.299 GOL.10: 4 residues within 4Å: Chain C: V.150, N.151, F.161, Q.177 2 PLIP interactions: 2 interactions with chain C Water bridges: C:N.151, C:N.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matthew, S. et al., Gatorbulin-1, a distinct cyclodepsipeptide chemotype, targets a seventh tubulin pharmacological site. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-03-03

Peptides

Tubulin alpha-1B chain: A
Tubulin beta-3 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-3 chain

Designed Ankyrin Repeat Protein (DARPIN) D1

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