SMTL ID : 4o4j.1

Tubulin-Peloruside A 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: 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.142, 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 32 PLIP interactions: 28 interactions with chain A, 4 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: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.10, A:G.13, A:F.141, A:T.145, A:T.145, A:A.174, A:T.179, A:T.179, 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.8: 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.9 27 PLIP interactions: 23 interactions with chain C, 4 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:G.13, C:E.71, C:N.101, C:F.141, C:T.179, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain B: Q.11 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain C: E.71 Chain D: K.252 Ligands: GTP.8 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain D: Q.11 Ligands: GDP.10 No protein-ligand interaction detected (PLIP)

1 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.39, A:D.39, A:G.44, A:E.55

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.158, G.162, K.166, E.196, H.197, S.198, D.199 Chain E: D.42 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:G.162, A:K.166, A:D.199, E:D.42 Water bridges: A:K.166

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

GDP.5: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, 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.6 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:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:N.99, B:S.138, B:G.140, B:G.140, B:T.143, B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222 GDP.10: 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.11 17 PLIP interactions: 17 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:G.140, D:G.140, D:G.141, D:S.145

2 x POU: Peloruside A(Non-covalent)

POU.7: 11 residues within 4Å: Chain B: Q.291, F.294, D.295, S.296, M.299, P.305, R.306, Y.310, V.333, N.337, Y.340 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:F.294, B:R.306, B:Y.310, B:V.333, B:N.337, B:Y.340 Hydrogen bonds: B:Q.291, B:D.295, B:D.295, B:S.296, B:R.306, B:Y.310 Water bridges: B:Q.291, B:N.337, B:N.337 POU.12: 9 residues within 4Å: Chain D: Q.291, F.294, D.295, S.296, P.305, R.306, Y.310, N.337, Y.340 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Q.291, D:Y.310, D:N.337, D:Y.340, D:Y.340 Hydrogen bonds: D:Q.291, D:D.295, D:S.296, D:K.297, D:R.306, D:Y.310 Water bridges: D:K.336, D:N.337 Salt bridges: D:R.306

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

ACP.13: 15 residues within 4Å: Chain F: K.74, Q.183, K.184, Y.185, L.186, K.198, D.200, L.240, T.241, N.242, D.318, M.320, I.330, E.331, N.333 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:K.74, F:Q.183, F:Q.183, F:L.186, F:K.198, F:D.200, F:T.241, F:N.242, F:E.331, F:N.333, F:N.333, F:N.333 Salt bridges: F:K.74 pi-Stacking: F:Y.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prota, A.E. et al., Structural basis of microtubule stabilization by laulimalide and peloruside A. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-03-26

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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