SMTL ID : 6bjc.1

TPX2_mini decorated GMPCPP-microtubule

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-6-6-2-mer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: 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 Chain I: K.252 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain I Hydrogen bonds: A:Q.11, A:A.12, A:Q.15, A:D.98, A:A.99, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.206, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: I:K.252, I:K.252, I:K.252 GTP.5: 22 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, T.179, E.183, N.206, Y.224, L.227, N.228 Chain M: K.252 Ligands: MG.6 22 PLIP interactions: 19 interactions with chain C, 3 interactions with chain M Hydrogen bonds: C:Q.11, C:A.12, C:Q.15, C:D.98, C:A.99, C:A.100, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: M:K.252, M:K.252, M:K.252 GTP.9: 22 residues within 4Å: Chain F: 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 Chain K: K.252 Ligands: MG.10 22 PLIP interactions: 19 interactions with chain F, 3 interactions with chain K Hydrogen bonds: F:Q.11, F:A.12, F:Q.15, F:D.98, F:A.99, F:A.100, F:N.101, F:S.140, F:G.144, F:T.145, F:T.145, F:G.146, F:E.183, F:N.206, F:N.206, F:N.228, F:N.228 pi-Stacking: F:Y.224, F:Y.224 Salt bridges: K:K.252, K:K.252, K:K.252 GTP.13: 22 residues within 4Å: Chain G: K.252 Chain H: 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.14 22 PLIP interactions: 19 interactions with chain H, 3 interactions with chain G Hydrogen bonds: H:Q.11, H:A.12, H:Q.15, H:D.98, H:A.99, H:A.100, H:N.101, H:S.140, H:G.144, H:T.145, H:T.145, H:G.146, H:E.183, H:N.206, H:N.206, H:N.228, H:N.228 pi-Stacking: H:Y.224, H:Y.224 Salt bridges: G:K.252, G:K.252, G:K.252 GTP.17: 22 residues within 4Å: Chain D: K.252 Chain J: 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.18 22 PLIP interactions: 19 interactions with chain J, 3 interactions with chain D Hydrogen bonds: J:Q.11, J:A.12, J:Q.15, J:D.98, J:A.99, J:A.100, J:N.101, J:S.140, J:G.144, J:T.145, J:T.145, J:G.146, J:E.183, J:N.206, J:N.206, J:N.228, J:N.228 pi-Stacking: J:Y.224, J:Y.224 Salt bridges: D:K.252, D:K.252, D:K.252 GTP.21: 22 residues within 4Å: Chain B: K.252 Chain L: 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.22 22 PLIP interactions: 19 interactions with chain L, 3 interactions with chain B Hydrogen bonds: L:Q.11, L:A.12, L:Q.15, L:D.98, L:A.99, L:A.100, L:N.101, L:S.140, L:G.144, L:T.145, L:T.145, L:G.146, L:E.183, L:N.206, L:N.206, L:N.228, L:N.228 pi-Stacking: L:Y.224, L:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252

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

MG.2: 2 residues within 4Å: Chain A: E.71 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.11, E.69 Ligands: G2P.3 No protein-ligand interaction detected (PLIP) 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.69 Ligands: G2P.7 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain G: Q.11, E.69 Ligands: G2P.11 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain I: Q.11, E.69 Ligands: G2P.15 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain J: E.71 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain K: Q.11, E.69 Ligands: G2P.19 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain L: E.71 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain M: Q.11, E.69 Ligands: G2P.23 No protein-ligand interaction detected (PLIP)

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

G2P.3: 16 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.4 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:A.97, B:G.98, B:N.99, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:E.181, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 G2P.7: 16 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.8 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:A.97, D:G.98, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:E.181, D:N.204, D:N.204, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 G2P.11: 16 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.12 19 PLIP interactions: 19 interactions with chain G Hydrogen bonds: G:Q.11, G:C.12, G:A.97, G:G.98, G:N.99, G:N.99, G:S.138, G:G.142, G:T.143, G:T.143, G:G.144, G:E.181, G:E.181, G:N.204, G:N.204, G:N.226, G:N.226 pi-Stacking: G:Y.222, G:Y.222 G2P.15: 17 residues within 4Å: Chain I: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.16 19 PLIP interactions: 19 interactions with chain I Hydrogen bonds: I:Q.11, I:C.12, I:A.97, I:G.98, I:N.99, I:N.99, I:S.138, I:G.142, I:T.143, I:T.143, I:G.144, I:E.181, I:E.181, I:N.204, I:N.204, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222 G2P.19: 17 residues within 4Å: Chain K: G.10, Q.11, C.12, Q.15, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.20 19 PLIP interactions: 19 interactions with chain K Hydrogen bonds: K:Q.11, K:C.12, K:A.97, K:G.98, K:N.99, K:N.99, K:S.138, K:G.142, K:T.143, K:T.143, K:G.144, K:E.181, K:E.181, K:N.204, K:N.204, K:N.226, K:N.226 pi-Stacking: K:Y.222, K:Y.222 G2P.23: 16 residues within 4Å: Chain M: G.10, Q.11, C.12, Q.15, A.97, N.99, S.138, G.141, G.142, T.143, G.144, E.181, N.204, Y.222, N.226 Ligands: MG.24 19 PLIP interactions: 19 interactions with chain M Hydrogen bonds: M:Q.11, M:C.12, M:A.97, M:G.98, M:N.99, M:N.99, M:S.138, M:G.142, M:T.143, M:T.143, M:G.144, M:E.181, M:E.181, M:N.204, M:N.204, M:N.226, M:N.226 pi-Stacking: M:Y.222, M:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Structural insight into TPX2-stimulated microtubule assembly. Elife (2017)

Release Date

2017-11-22

Peptides

Tubulin alpha-1B chain: ACFHJL
Tubulin beta chain: BDGIKM
Targeting protein for Xklp2: EN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

F
E

H
J

J
L

L
K

B
B

D
D

G
F

I
H

K
G

M
I

E
T

N
P

Tubulin alpha-1B chain

Tubulin beta chain

Targeting protein for Xklp2

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