SMTL ID : 9c13.1

XMAP215 TOG5 interaction with GMPCPP tubulin lattice

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.89 Å

Oligo State

hetero-2-2-1-mer

Ligands

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

G2P.1: 18 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:A.97, A:N.99, A:S.138, A:G.142, A:T.143, A:T.143, A:G.144, A:D.177, A:E.181, A:N.204, A:N.204, A:N.226, A:N.226 pi-Stacking: A:Y.222, A:Y.222 G2P.3: 17 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, N.226 Ligands: MG.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:A.97, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

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

MG.2: 2 residues within 4Å: Chain A: D.67 Ligands: G2P.1 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Ligands: G2P.3 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: K.252 Chain C: Q.11, E.71 Ligands: GTP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.71 MG.8: 4 residues within 4Å: Chain B: K.252 Chain D: Q.11, E.71 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.71

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

GTP.5: 25 residues within 4Å: Chain A: L.246, K.252 Chain C: G.10, Q.11, A.12, Q.15, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, L.227, N.228 Ligands: MG.6 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:A.99, C:A.100, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:T.179, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 pi-Cation interactions: C:Y.224 Salt bridges: A:K.252, A:K.252, A:K.252 GTP.7: 23 residues within 4Å: Chain B: L.246, K.252 Chain D: 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, T.179, E.183, N.206, Y.224, L.227, N.228 Ligands: MG.8 23 PLIP interactions: 21 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:Q.11, D:A.12, D:Q.15, D:D.98, D:A.99, D:A.100, D:N.101, D:S.140, D:G.144, D:T.145, D:T.145, D:G.146, D:T.179, D:E.183, D:N.206, D:N.206, D:N.228, D:N.228 pi-Stacking: D:Y.224, D:Y.224 pi-Cation interactions: D:Y.224 Salt bridges: B:K.252, B:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McManus, C.T. et al., Structure and function of XMAP215s C terminal domains in microtubule nucleation. To Be Published

Release Date

2025-11-05

Peptides

Tubulin beta-2B chain: AB
Tubulin alpha chain: CD
Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
A

D
C

E
E

Tubulin beta-2B chain

Tubulin alpha chain

Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein

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