SMTL ID : 5fnv.1

a new complex structure of tubulin with an alpha-beta unsaturated lactone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-2-2-1-1-mer

Ligands

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

GTP.1: 26 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, T.179, E.183, N.206, Y.224, L.227, N.228, I.231 Chain B: K.252 Ligands: MG.2 30 PLIP interactions: 26 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, 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:E.71, A:E.71, A:S.140, A:F.141, A:T.145, A:T.145, A:A.174, 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.9: 26 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, L.227, 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: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:E.71, C:F.141, C:T.145, C:T.145, C:E.183, D:K.252, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.13: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, D.67, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, P.171, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.14 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:Q.11, D:C.12, D:A.97, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: 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: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain D: Q.11, D.67, E.69 Ligands: GTP.13 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 5 residues within 4Å: Chain A: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.39, A:T.41, A:T.41, A:G.44, A:E.55 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: 5 residues within 4Å: Chain C: D.39, T.41, G.44, G.45, E.55 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.39, C:T.41, C:T.41, C:G.44, C:E.55

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

GDP.4: 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.5 25 PLIP interactions: 25 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:N.99, B:S.138, B:G.141, B:G.142, B:T.143, B:T.143, B:G.144, B:V.175, B:D.177, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 Water bridges: B:D.67, B:S.138, B:G.140, B:T.143, B:S.145, B:S.145 pi-Stacking: B:Y.222, B:Y.222

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

MES.7: 11 residues within 4Å: Chain A: W.407 Chain B: R.156, P.160, D.161, R.162, M.164, E.194, N.195, T.196, D.197, R.251 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:D.197, B:R.251 MES.8: 8 residues within 4Å: Chain B: F.294, D.295, A.296, D.304, R.306, V.333, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.296, B:D.304 Salt bridges: B:R.306

1 x X3H: PIRONETIN(Covalent)

X3H.12: 12 residues within 4Å: Chain C: C.4, L.136, L.167, I.238, S.241, L.242, F.255, C.316, L.317, L.318, C.376, L.378 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.136, C:L.167, C:L.167, C:L.378 Hydrogen bonds: C:S.241

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

ACP.15: 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, L.240, T.241, N.242, D.318, I.330, E.331, N.333 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:K.74, F:K.150, F:Q.183, F:L.186, F:K.198, F:D.200, F:R.222, F:R.222, F:T.241, F:T.241, F:T.241, 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

Yang, J. et al., Pironetin Reacts Covalently with Cysteine-316 of Alpha-Tubulin to Destabilize Microtubule. Nat.Commun. (2016)

Release Date

2016-05-18

Peptides

TUBULIN ALPHA-1B CHAIN: AC
TUBULIN BETA 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 CHAIN

STATHMIN-4

TUBULIN TYROSINE LIGASE

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