SMTL ID : 5sbc.1

Tubulin-maytansinoid-5a-complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 24 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, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 28 PLIP interactions: 24 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, 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.206, A:N.228 Water bridges: A:Q.11, A:Q.11, A:E.71, A:S.140, A:F.141, 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.9: 24 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, N.228, I.231 Chain D: K.252 Ligands: MG.10 28 PLIP interactions: 24 interactions with chain C, 4 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.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 Water bridges: C:G.13, C:E.71, C:F.141, C:T.145, C:T.145, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.4 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.13 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain F: E.331, N.333 Ligands: ACP.17 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:D.39, A:G.44, A:E.55, H2O.3 CA.6: 1 residues within 4Å: Chain B: E.111 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.111 CA.11: 4 residues within 4Å: Chain C: D.39, T.41, G.44, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:T.41, C:E.55, C:E.55, H2O.13 CA.16: 1 residues within 4Å: Chain E: D.42 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.42

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

GDP.4: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.141, G.142, T.143, G.144, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.5 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:T.143, B:G.144, B:V.175, B:E.181, B:N.204, B:N.204, B:N.204, B:N.226 Water bridges: B:Q.15, B:G.98, B:S.138, B:L.139, B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.13: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226 Ligands: MG.14 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:E.181, D:N.204, D:N.204, D:N.204, D:N.226 Water bridges: D:G.13, D:N.99, D:S.138, D:S.145 pi-Stacking: D:Y.222, D:Y.222

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

MES.7: 10 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, D.197, R.251 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.162 Water bridges: B:R.156, B:R.251, A:R.105, A:R.105 Salt bridges: B:D.197, B:R.251

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain B: V.175, S.176, P.220, T.221, Y.222 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.176 Water bridges: B:S.176

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.12: 4 residues within 4Å: Chain C: Y.262, I.265, D.431, V.435 1 PLIP interactions: 1 interactions with chain C pi-Stacking: C:Y.262

1 x 5JS: (1S,2R,3S,5S,6S,16E,18E,20R)-11-chloro-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18,21-hexaen-6-yl phenylacetate(Non-covalent)

5JS.15: 10 residues within 4Å: Chain D: G.98, N.99, N.100, K.103, D.177, T.178, V.179, V.180, F.394, W.397 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.179, D:W.397, D:W.397, D:W.397, D:W.397 Hydrogen bonds: D:N.99, D:N.100, D:K.103, D:V.179

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

ACP.17: 19 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, R.202, R.222, H.239, T.241, N.242, D.318, I.330, E.331, N.333 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:R.202, F:R.222, F:T.241, F:T.241, F:N.242, F:N.333, F:N.333, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marzullo, P. et al., Maytansinol Derivatives: Side Reactions as a Chance for New Tubulin Binders. Chemistry (2022)

Release Date

2021-12-08

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B 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-2B chain

Stathmin-4

Tubulin-Tyrosine Ligase

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