SMTL ID : 5kx5.1

Crystal structure of tubulin-stathmin-TTL-Compound 11 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-oligomer

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, 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:A.99, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.206, A:N.228 Water bridges: A:G.13 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.9: 25 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, 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, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.10 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.206, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252

6 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) MG.5: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain B: D.295, S.296 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.296, H2O.2 MG.10: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 5 residues within 4Å: Chain D: S.176, T.178, E.181 Ligands: GDP.12, MG.14 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain D: Q.11, N.99 Ligands: GDP.12, MG.13 No protein-ligand interaction detected (PLIP)

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:T.41, A:T.41, A:G.44, A:E.55 CA.6: 1 residues within 4Å: Chain B: E.111 No protein-ligand interaction detected (PLIP) CA.11: 6 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, D.47, E.55 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.39, C:D.39, C:T.41, C:E.55 CA.16: 3 residues within 4Å: Chain A: S.158, E.196 Chain E: D.42 No protein-ligand interaction detected (PLIP)

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

GDP.4: 18 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.5, 6YK.7 19 PLIP interactions: 19 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:N.204, B:N.226 Water bridges: B:A.97, B:A.97, B:S.138, B:L.139 pi-Stacking: B:Y.222, B:Y.222 GDP.12: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.13, MG.14, 6YK.15 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.204, D:N.226 pi-Stacking: D:Y.222, D:Y.222

2 x 6YK: (2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,2-dimethylpyrrolidin-2-yl]carbonylamino]-3-methyl-pentanoyl]-methyl-amino]-4-methyl-pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-aminophenyl)-2-methyl-pentanoic acid(Non-covalent)

6YK.7: 22 residues within 4Å: Chain B: Q.11, Q.15, P.173, K.174, V.175, D.177, T.219, P.220, T.221, Y.222, G.223, L.225, R.276 Chain C: L.248, P.325, V.328, N.329, I.332, F.351, V.353, I.355 Ligands: GDP.4 21 PLIP interactions: 8 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:L.248, C:P.325, C:V.328, C:I.332, C:V.353, C:I.355, B:Q.15, B:T.219, B:T.221, B:Y.222, B:Y.222, B:L.225 Hydrogen bonds: C:N.329, C:N.329, B:Q.11, B:T.221, B:Y.222, B:G.223 Water bridges: B:Q.15 Salt bridges: B:D.177, B:R.276 6YK.15: 14 residues within 4Å: Chain D: Q.11, Q.15, K.174, V.175, S.176, D.177, T.219, P.220, T.221, Y.222, G.223, L.225, R.276 Ligands: GDP.12 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:Q.15, D:T.219, D:T.221, D:Y.222, D:Y.222, D:Y.222, D:L.225 Hydrogen bonds: D:Q.11, D:Q.15, D:T.221, D:Y.222, D:G.223 Salt bridges: D:R.276

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.17: 17 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:K.150, F:Q.183, F:L.186, F:K.198, F:T.241, F:T.241, F:N.242 Salt bridges: F:K.74, F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leverett, C.A. et al., Design, Synthesis, and Cytotoxic Evaluation of Novel Tubulysin Analogues as ADC Payloads. ACS Med Chem Lett (2016)

Release Date

2016-12-28

Peptides

Tubulin alpha chain: AC
Tubulin beta chain: BD
Stathmin-4: E
TTL protein: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Tubulin alpha chain

Tubulin beta chain

Stathmin-4

TTL protein

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