SMTL ID : 6y4m.1

Structure of Tubulin Tyrosine Ligase in Complex with Tb111

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 25 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, N.228, I.231 Chain B: K.252 Ligands: MG.2 24 PLIP interactions: 20 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: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:T.145, A:T.145, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.10: 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, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.11 22 PLIP interactions: 19 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: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:T.145, C:T.145, D:K.252, D:K.252 pi-Stacking: C:Y.224 Salt bridges: D:K.252 GTP.15: 22 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, 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 Ligands: MG.16 21 PLIP interactions: 21 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:E.69, D:E.69, D:T.143 pi-Stacking: D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

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: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: D.69, E.71 Ligands: GTP.10 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain D: Q.11 Ligands: GTP.15 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 8 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, D.47, F.49, N.50, 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: 6 residues within 4Å: Chain C: D.39, T.41, G.44, D.47, N.50, 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, OH5.9 17 PLIP interactions: 17 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:S.176, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:S.138, B:S.138

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

MES.6: 11 residues within 4Å: Chain B: R.156, P.160, D.161, R.162, I.163, M.164, E.194, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B 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: O9H.8, VAL.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.332, C:V.353 Water bridges: C:V.353 Salt bridges: B:D.177

1 x O9H: [(1~{R},3~{R})-1-acetyloxy-1-[4-methanoyl-5-(2-phenylmethoxyethyl)-2,3-dihydro-1,3-thiazol-2-yl]-4-methyl-pentan-3-yl]-methyl-azanium(Non-covalent)

O9H.8: 16 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: A.247, L.248, P.325, Y.357 Ligands: O9B.7, OH5.9, VAL.14 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:A.247, C:L.248, C:P.325, B:V.175, B:Y.208, B:T.219, B:L.225 Hydrogen bonds: B:Y.222, B:G.223

1 x OH5: (2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid(Non-covalent)

OH5.9: 8 residues within 4Å: Chain B: Q.15, T.221, Y.222, G.223, N.226, R.276 Ligands: GDP.4, O9H.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.15, B:Y.222, B:Y.222 Hydrogen bonds: B:T.221, B:G.223 Salt bridges: B:R.276

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

PGE.13: 6 residues within 4Å: Chain B: R.391 Chain C: Y.262, R.264, I.265, D.431, E.434 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.391, B:R.391, C:R.264

1 x VAL: VALINE(Non-covalent)

VAL.14: 6 residues within 4Å: Chain C: L.248, P.325, N.329, V.353 Ligands: O9B.7, O9H.8 5 PLIP interactions: 5 interactions with chain C, Hydrophobic interactions: C:L.248, C:P.325, C:V.353 Hydrogen bonds: C:N.329, C:N.329

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

ACP.17: 19 residues within 4Å: Chain F: K.74, K.150, I.160, 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, I.330, E.331, N.333 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:D.200, F:R.202, F:R.222, F:R.222, F:T.241, F:T.241, F:N.242, F:N.242, F:D.318, F:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

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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