SMTL ID : 5ezy.1

Crystal structure of T2R-TTL-taccalonolide AJ complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 31 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, N.102, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 26 PLIP interactions: 21 interactions with chain A, 5 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:T.145, A:G.146, A:N.206, A:N.206, A:N.228, A:N.228 Water bridges: A:E.71, A:N.101, A:S.140, A:F.141, 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.9: 30 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, I.171, P.173, A.174, V.177, S.178, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain D: K.252 Ligands: MG.10 28 PLIP interactions: 23 interactions with chain C, 5 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:T.145, C:G.146, C:N.206, C:N.206, C:Y.224, C:N.228, C:N.228 Water bridges: C:G.13, C:F.141, C:T.179, C:E.183, 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 GTP.12: 29 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, G.96, A.97, G.98, N.99, N.100, S.138, G.140, G.141, G.142, T.143, G.144, V.169, P.171, S.172, V.175, S.176, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.13 26 PLIP interactions: 26 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:G.144, D:S.176, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 Water bridges: D:G.13, D:N.99, D:G.140, D:S.145, D:S.145, D:S.176, D:E.181 pi-Stacking: D:Y.222, D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.98 Chain B: K.252 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: 5 residues within 4Å: Chain C: Q.11, E.71, D.98 Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: Q.11, E.69 Ligands: GTP.12 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, F.49, 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.1 CA.11: 6 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, F.49, E.55 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.39, C:D.39, C:G.44, C:E.55, H2O.24

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

GDP.4: 27 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, A.97, S.138, G.140, G.141, G.142, T.143, G.144, S.145, V.169, P.171, S.172, V.175, S.176, D.177, E.181, N.204, L.207, Y.222, L.225, N.226, V.229 Ligands: MG.5 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:A.97, B:G.140, B:G.140, B:G.141, B:T.143, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222

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

MES.6: 12 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, I.163, M.164, E.194, N.195, T.196, D.197, R.251 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.156, B:P.160, B:R.251 Salt bridges: B:D.197, B:R.251 MES.7: 11 residues within 4Å: Chain B: F.294, D.295, S.296, D.304, P.305, R.306, Y.310, V.333, N.337, Y.340, F.341 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.295, B:S.296 Water bridges: B:F.294, B:D.295 Salt bridges: B:R.306

2 x TAJ: taccalonolide AJ(Covalent)

TAJ.8: 14 residues within 4Å: Chain B: K.19, L.215, L.217, T.221, G.223, D.224, H.227, L.228, F.270, T.274, S.275, R.276, G.360, L.361 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.215, B:H.227 Water bridges: B:T.221 Salt bridges: B:K.19, B:H.227, B:H.227, B:R.276, B:R.276 TAJ.14: 15 residues within 4Å: Chain D: K.19, L.215, L.217, T.221, G.223, D.224, H.227, L.228, L.273, T.274, S.275, R.276, Q.280, G.360, L.361 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.215, D:H.227, D:R.276 Water bridges: D:H.227, D:H.227 Salt bridges: D:K.19, D:H.227

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

ACP.15: 21 residues within 4Å: Chain F: K.74, P.95, 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, M.320, I.330, E.331, N.333 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:R.222, F:T.241, F:T.241, F:T.241, F:N.242, F:E.331, F:E.331 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., Mechanism of microtubule stabilization by taccalonolide AJ. Nat Commun (2017)

Release Date

2017-01-11

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
Stathmin-4: E
Uncharacterized protein: 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

Uncharacterized protein

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