SMTL ID : 5lxs.1

Tubulin-KS-1-199-32 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 23 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, 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: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:G.13, A:E.71, A:F.141, 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, B:K.252 GTP.9: 23 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, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.10 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:Q.15, C:A.99, 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:E.71, C:F.141, C:T.145, C:T.145, C:E.183, 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: 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.10: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.12 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain F: K.74, E.331, N.333 Ligands: ACP.16 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:T.41, A:G.44, A:E.55, H2O.2 CA.6: 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.11 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:G.44, C:E.55, H2O.14 CA.15: 1 residues within 4Å: 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, I.16, 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.226, B:N.226 Water bridges: B:G.13, B:L.139, B:G.140, B:G.141, B:T.143, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.12: 17 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.13 22 PLIP interactions: 22 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.226, D:N.226 Water bridges: D:S.138, D:S.138, D:G.140, D:G.141, D:G.141, D:T.143, D:T.143, D:S.172, D:S.176, D:E.181

2 x 7AO: [(3~{Z},5~{S},6~{S},7~{S},8~{R},9~{S},11~{Z},13~{S},14~{S},15~{S},16~{Z},18~{S})-19-[(2~{S},3~{R},4~{S},5~{R})-3,5-dimethyl-4-oxidanyl-6-oxidanylidene-oxan-2-yl]-5,7,9,11,13,15-hexamethyl-8,14,18-tris(oxidanyl)nonadeca-1,3,11,16-tetraen-6-yl] ~{N}-[3-[(3-azidophenyl)carbonylamino]propyl]carbamate(Non-covalent)

7AO.7: 15 residues within 4Å: Chain B: L.215, D.224, H.227, A.231, F.270, P.272, L.273, T.274, S.275, R.276, Q.280, Y.281, R.359, G.360, L.361 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:H.227, B:A.231, B:F.270, B:L.273, B:R.276 Hydrogen bonds: B:D.224, B:H.227, B:T.274, B:T.274, B:T.274, B:R.359, B:G.360, B:G.360 Water bridges: B:L.361, B:L.361 Salt bridges: B:H.227 7AO.14: 15 residues within 4Å: Chain D: C.211, L.215, D.224, H.227, L.228, A.231, P.272, L.273, T.274, R.276, Q.279, Q.280, R.359, G.360, L.361 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.228, D:A.231, D:L.273, D:Q.279, D:Q.280 Hydrogen bonds: D:D.224, D:T.274, D:T.274, D:Q.279, D:R.359 Salt bridges: D:H.227

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

MES.8: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, N.195, T.196, D.197, R.251 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Water bridges: A:R.105, B:R.156 Salt bridges: B:D.197, B:R.251

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

ACP.16: 21 residues within 4Å: Chain F: K.74, I.148, K.150, I.160, Q.183, K.184, Y.185, L.186, K.198, D.200, R.222, H.239, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 Ligands: MG.17 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, 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:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prota, A.E. et al., Structural Basis of Microtubule Stabilization by Discodermolide. Chembiochem (2017)

Release Date

2017-09-20

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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