SMTL ID : 6y4n.1

Structure of Tubulin Tyrosine Ligase in Complex with Tb116

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 27 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 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:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:S.140, A:T.145, A:T.145, A:E.183, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 27 residues within 4Å: Chain C: 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.11 27 PLIP interactions: 24 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 Water bridges: C:G.13, C:G.142, C:T.145, C:T.145, C:A.174, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.16: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.96, 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, Y.222, N.226 Ligands: MG.17 24 PLIP interactions: 24 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:A.97, D:A.97, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:E.69, D:S.138, D:G.141, D:T.143, D:T.143, D:S.145 pi-Stacking: D:Y.222, D:Y.222

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: D.69, E.71 Chain B: K.252 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.11: 4 residues within 4Å: Chain C: D.69, E.71 Chain D: K.252 Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Ligands: GTP.16 No protein-ligand interaction detected (PLIP) MG.20: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.19 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, D.47, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:D.39, A:T.41, A:G.44, A:E.55 CA.12: 5 residues within 4Å: Chain C: D.39, T.41, G.44, D.47, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:D.39, C:T.41, C:G.44, C:E.55

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

GDP.4: 20 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.169, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.5, O9N.9 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, 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:N.226, B:N.226 Water bridges: B:E.69, B:S.138, B:G.140, B:G.141, B:T.143, B:S.145, B:S.176 pi-Stacking: B:Y.222, B:Y.222

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.6: 10 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.156 Salt bridges: B:D.197, B:R.251

1 x O9B: (2~{R})-1-methylpiperidine-2-carboxylic acid(Non-covalent)

O9B.7: 10 residues within 4Å: Chain B: P.173, K.174, V.175, D.177 Chain C: N.329, I.332, F.351, V.353 Ligands: O9K.8, VAL.14 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.332, C:V.353 Salt bridges: B:D.177

1 x O9K: [(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate(Non-covalent)

O9K.8: 15 residues within 4Å: Chain B: K.174, V.175, Y.208, T.219, P.220, T.221, Y.222, G.223, L.225 Chain C: L.248, P.325 Ligands: O9B.7, O9N.9, VAL.14, P6S.15 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.175, B:Y.208, B:T.219, B:T.221, B:Y.222, B:L.225, C:P.325 Hydrogen bonds: B:Y.222, B:G.223 Water bridges: B:T.221

1 x O9N: methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate(Non-covalent)

O9N.9: 7 residues within 4Å: Chain B: Q.11, Q.15, Y.222, N.226 Ligands: GDP.4, O9K.8, P6S.15 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.15, B:Y.222 Water bridges: B:T.221, B:T.221, B:R.276

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.13: 5 residues within 4Å: Chain C: Y.262, P.263, R.264, D.431, E.434 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.264, C:D.431, C:E.434, C:E.434

1 x VAL: VALINE(Non-covalent)

VAL.14: 7 residues within 4Å: Chain C: L.248, P.325, N.329, V.353, I.355 Ligands: O9B.7, O9K.8 6 PLIP interactions: 6 interactions with chain C, Hydrophobic interactions: C:L.248, C:P.325, C:V.353, C:I.355 Hydrogen bonds: C:N.329, C:N.329

1 x P6S: benzyl hydrogen carbonate(Non-covalent)

P6S.15: 5 residues within 4Å: Chain C: L.248, P.325, Y.357 Ligands: O9K.8, O9N.9 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.248

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 3 residues within 4Å: Chain D: P.220, T.221, Y.222 No protein-ligand interaction detected (PLIP)

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.19: 20 residues within 4Å: Chain F: K.74, I.148, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 Ligands: MG.20 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:K.74, F:K.184, F:L.186, F:K.198, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:D.318, F:D.318, F:N.333 Water bridges: F:R.202, F:N.333 Salt bridges: F:K.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicolaou, K.C. et al., Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis. J.Org.Chem. (2021)

Release Date

2021-03-31

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta chain: BD
Stathmin-4: E
Tubulin-Tyrosine Ligase: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

F
F

Tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Tubulin-Tyrosine Ligase

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