SMTL ID : 8yrk.1

Tubulin-Compound KY216: stathmin-like domain complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 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.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 B: K.252 Ligands: MG.2 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.98, A:D.98, 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:E.71, A:E.71, A:T.145, B:K.252, B:K.252 pi-Stacking: 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.14 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, C:N.101, 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:E.71, C:D.98, C:T.145, 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: E.71 Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: Q.11, D.177 Ligands: GDP.5 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: E.71, D.98 Chain D: K.252 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain D: D.67, E.69 Ligands: GDP.15 No protein-ligand interaction detected (PLIP)

2 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: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.39, A:G.44, A:E.55, A:E.55, H2O.1 CA.12: 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:D.39, C:G.44, C:E.55, C:E.55

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: Y.161, G.162, K.163, K.164 Ligand excluded by PLIP

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

GDP.5: 18 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, P.171, V.175, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.6 18 PLIP interactions: 18 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.141, B:S.145, B:D.177 pi-Stacking: B:Y.222, B:Y.222 GDP.15: 17 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, P.171, V.175, S.176, E.181, N.204, Y.222, N.226 Ligands: MG.16 15 PLIP interactions: 15 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:S.176, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D: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: 7 residues within 4Å: Chain B: F.294, D.295, S.296, R.306, V.333, N.337, Y.340 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.295, B:S.296 Salt bridges: B:R.306

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 3 residues within 4Å: Chain B: D.114, D.118, R.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.118

2 x 01: (11R,16S)-11-(3,5-dichloro-4-methoxyphenyl)-4,7-dioxa-12,14-diazatetracyclo[8.7.0.03,8.012,16]heptadeca-1,3(8),9-triene-13,15-dione

01.10: 15 residues within 4Å: Chain B: V.236, C.239, L.246, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, A.315, N.348, K.350, A.352 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.248, B:L.253, B:N.256, B:K.350 Hydrogen bonds: B:N.247, B:D.249 Halogen bonds: B:A.315 01.17: 17 residues within 4Å: Chain C: T.179 Chain D: V.236, C.239, L.246, A.248, D.249, K.252, L.253, N.256, M.257, V.313, A.314, A.315, I.316, N.348, K.350, A.352 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:L.246, D:L.253, D:N.256, D:K.350 Hydrogen bonds: D:N.247, D:D.249 Halogen bonds: D:A.315

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.13: 6 residues within 4Å: Chain C: C.4, Q.133, G.134, F.135, S.165, L.167 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.135, C:Q.256

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

ACP.18: 15 residues within 4Å: Chain F: K.74, I.148, K.150, Q.183, K.184, Y.185, L.186, K.198, D.200, H.239, T.241, D.318, I.330, E.331, N.333 12 PLIP interactions: 12 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:D.200, F:T.241, F:D.318, F:N.333 Salt bridges: F:K.74, F:K.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xia, Y.Z. et al., Tubulin-Compound KY216: stathmin-like domain complex. To Be Published

Release Date

2025-04-02

Peptides

Detyrosinated 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

Detyrosinated tubulin alpha-1B chain

Tubulin beta chain

Stathmin-4

Tubulin tyrosine ligase

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