SMTL ID : 8b7a.1

Tubulin - maytansinoid - 4 complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 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 31 PLIP interactions: 26 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, 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:G.13, A:E.71, A:N.101, A:F.141, A:T.145, A:A.174, B:K.252, B:K.252, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.11: 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.12 32 PLIP interactions: 26 interactions with chain C, 6 interactions with chain D Hydrogen bonds: 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.228, C:N.228 Water bridges: C:Q.11, C:Q.11, C:G.13, C:N.101, C:F.141, C:T.145, C:T.145, D:Q.245, D:K.252, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

6 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 A: G.162, K.164, D.199 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.6 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.14 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain F: E.331, N.333 Ligands: ACP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.331

5 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:T.41, A:G.44, A:E.55, H2O.2 CA.8: 1 residues within 4Å: Chain B: E.111 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.111, H2O.9 CA.10: 1 residues within 4Å: Chain B: D.118 No protein-ligand interaction detected (PLIP) CA.13: 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:G.44, C:E.55, C:E.55, H2O.16 CA.17: 1 residues within 4Å: Chain E: D.42 No protein-ligand interaction detected (PLIP)

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 6 residues within 4Å: Chain A: N.216, A.273, P.274, V.275, A.294, N.300 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.216, A:V.275 Water bridges: A:Y.272, A:N.300, A:N.300

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

GDP.6: 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, D.177, E.181, N.204, L.207, Y.222, N.226 Ligands: MG.7 24 PLIP interactions: 24 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.226, B:N.226 Water bridges: B:G.13, B:E.69, B:E.69, B:G.98, B:N.99, B:L.139, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.14: 20 residues within 4Å: Chain D: 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, L.225, N.226 Ligands: MG.15 20 PLIP interactions: 20 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:T.143, D:G.144, D:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 Water bridges: D:G.13, D:S.138, D:G.140, D:G.140, D:G.141, D:S.145

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

MES.9: 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 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.156, B:R.251, A:R.105 Salt bridges: B:D.197, B:R.251

1 x Q0F: [(1~{R},2~{R},3~{S},5~{S},6~{S},16~{E},18~{E},20~{R},21~{S})-11-chloranyl-12,20-dimethoxy-2,5,9,16-tetramethyl-21-oxidanyl-8,23-bis(oxidanylidene)-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1^{10,14}.0^{3,5}]hexacosa-10(26),11,13,16,18-pentaen-6-yl] pent-4-enoate(Non-covalent)

Q0F.16: 9 residues within 4Å: Chain D: G.98, N.99, N.100, K.103, T.178, V.179, V.180, F.394, W.397 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:N.100, D:V.179, D:F.394, D:W.397, D:W.397, D:W.397 Hydrogen bonds: D:N.99, D:N.100, D:V.179 Water bridges: D:K.103

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

ACP.18: 20 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, L.240, T.241, N.242, D.318, I.330, E.331, N.333 Ligands: MG.19 16 PLIP interactions: 16 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.242, F:D.318, F:E.331, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boiarska, Z. et al., Maytansinol Functionalization: Towards Useful Probes for Studying Microtubule Dynamics. Chemistry (2023)

Release Date

2023-08-23

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

Related Entries With Identical Sequence