SMTL ID : 7dmz.1

GMPCPP microtubule complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

GTP.1: 18 residues within 4Å: Chain A: Q.11, A.12, Q.15, I.16, D.69, E.71, D.98, A.99, A.100, S.140, G.143, T.145, I.171, E.183, N.206, Y.224, N.228 Chain E: K.252 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain E Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:Q.15, A:D.69, A:E.71, A:A.99, A:A.100, A:S.140, A:E.183, A:N.206, A:N.228, A:N.228 Salt bridges: E:K.252, E:K.252, E:K.252 GTP.2: 18 residues within 4Å: Chain B: Q.11, A.12, Q.15, E.71, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, T.179, E.183, N.206, Y.224, N.228 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:A.12, B:Q.15, B:A.99, B:A.100, B:N.101, B:S.140, B:G.143, B:G.144, B:T.145, B:G.146, B:T.179, B:E.183, B:N.206, B:N.206, B:N.228, B:N.228 GTP.4: 18 residues within 4Å: Chain C: Q.11, A.12, Q.15, E.71, D.98, A.100, G.143, G.144, T.145, G.146, I.171, N.206, Y.224, N.228 Chain D: L.246, N.247, K.252 Ligands: MG.5 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.11, C:A.100, C:G.144, C:T.145, C:G.146, C:T.179, C:T.179, C:N.206, C:N.228, C:N.228, C:N.228, D:N.247 pi-Cation interactions: C:Y.224 Salt bridges: D:K.252, D:K.252, D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.2 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain C: T.145 Ligands: GTP.4 No protein-ligand interaction detected (PLIP)

3 x TAJ: taccalonolide AJ(Covalent)

TAJ.6: 7 residues within 4Å: Chain D: K.19, G.223, D.224, H.227, R.276, R.359, L.361 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.224, D:H.227 Hydrogen bonds: D:K.19 Salt bridges: D:K.19, D:H.227, D:R.276 TAJ.8: 8 residues within 4Å: Chain E: K.19, L.215, T.221, G.223, D.224, H.227, L.228, R.359 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:L.215, E:D.224, E:H.227 Hydrogen bonds: E:K.19 Salt bridges: E:K.19, E:H.227, E:H.227 TAJ.10: 9 residues within 4Å: Chain F: K.19, L.215, L.217, G.223, D.224, H.227, R.359, G.360, L.361 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:L.215, F:L.217, F:D.224, F:H.227, F:L.361 Hydrogen bonds: F:K.19 Salt bridges: F:K.19, F:H.227

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

G2P.7: 14 residues within 4Å: Chain B: A.247, L.248 Chain D: G.10, Q.11, C.12, D.67, E.69, S.138, G.141, G.142, T.143, N.204, Y.222, N.226 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.11, D:E.69, D:N.99, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:N.204, D:Y.222, D:N.226, D:N.226 G2P.9: 12 residues within 4Å: Chain E: Q.11, C.12, N.99, S.138, G.140, G.141, G.142, T.143, G.144, D.177, Y.222, N.226 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Q.11, E:N.99, E:S.138, E:G.142, E:T.143, E:T.143, E:G.144, E:D.177, E:N.226, E:N.226, E:N.226 pi-Stacking: E:Y.222 G2P.11: 13 residues within 4Å: Chain A: E.254 Chain F: Q.11, C.12, Q.15, I.16, E.69, N.99, G.141, T.143, D.177, N.204, Y.222, N.226 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:E.69, F:E.69, F:N.99, F:S.138, F:T.143, F:T.143, F:D.177, F:N.204, F:N.226, F:N.226, F:N.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2021-12-08

Peptides

Tubulin alpha-1B chain: ABC
Tubulin beta chain: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

C
B

D
E

E
C

F
F

Tubulin alpha-1B chain

Tubulin beta chain

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