SMTL ID : 7dn0.1

AJ-GMPCPP-MT-non-seam

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

GTP.1: 17 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, A.99, N.101, S.140, G.143, G.144, T.145, T.179, E.183, N.206, Y.224, L.227, N.228 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:Q.15, A:A.99, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:N.206, A:N.228 pi-Cation interactions: A:Y.224 GTP.3: 20 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, L.227, N.228 Chain F: K.252 Ligands: MG.4 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain F Hydrogen bonds: B:Q.11, B:Q.15, B:A.99, B:N.101, B:S.140, B:G.144, B:T.145, B:G.146, B:E.183, B:N.206, B:N.206, B:N.206 pi-Stacking: B:Y.224 pi-Cation interactions: B:Y.224 Salt bridges: F:K.252, F:K.252 GTP.5: 19 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, N.206, Y.224, L.227, N.228 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Q.11, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:G.146, C:N.206, C:N.206, C:N.206, C:N.228 pi-Cation interactions: C:Y.224 GTP.7: 19 residues within 4Å: Chain D: G.10, Q.11, Q.15, D.98, A.99, A.100, N.101, S.140, G.142, G.143, G.144, T.145, G.146, E.183, N.206, Y.224, N.228 Chain E: K.252 Ligands: MG.8 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Q.11, D:Q.15, D:A.99, D:A.100, D:N.101, D:N.101, D:S.140, D:G.144, D:T.145, D:G.146, D:E.183, D:N.206, D:N.206, D:N.228 pi-Stacking: D:Y.224 pi-Cation interactions: D:Y.224 Salt bridges: E:K.252

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.4: 4 residues within 4Å: Chain B: Q.11, E.71 Chain F: N.247 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71 MG.6: 2 residues within 4Å: Chain C: E.71 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.11, E.71 Ligands: GTP.7 No protein-ligand interaction detected (PLIP)

2 x G2P: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

G2P.9: 16 residues within 4Å: Chain C: L.248 Chain E: G.10, Q.11, C.12, Q.15, N.99, S.138, G.140, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:Q.11, E:C.12, E:N.99, E:S.138, E:G.142, E:T.143, E:T.143, E:G.144, E:D.177, E:N.204, E:N.204, E:N.226, E:N.226 pi-Stacking: E:Y.222 pi-Cation interactions: E:Y.222 G2P.11: 14 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, D.177, N.204, Y.222, N.226 16 PLIP interactions: 15 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:Q.11, F:C.12, F:N.99, F:S.138, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:D.177, F:N.204, F:N.204, F:N.226, F:N.226, A:E.254 pi-Cation interactions: F:Y.222

2 x TAJ: taccalonolide AJ(Covalent)

TAJ.10: 8 residues within 4Å: Chain E: K.19, L.215, L.217, D.224, F.270, T.274, R.276, R.359 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:L.215, E:L.215, E:L.217, E:F.270 Hydrogen bonds: E:K.19 Salt bridges: E:K.19, E:H.227, E:R.276 TAJ.12: 9 residues within 4Å: Chain F: K.19, L.215, G.223, D.224, H.227, L.273, T.274, R.276, R.359 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:L.215, F:L.215, F:H.227, F:L.273 Hydrogen bonds: F:K.19 Salt bridges: F:K.19, F:H.227, F:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y.X., GMPCPP microtubule. To Be Published

Release Date

2021-12-08

Peptides

Tubulin alpha-1B chain: ABCD
Tubulin beta chain: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
C

E
E

F
F

Tubulin alpha-1B chain

Tubulin beta chain

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