SMTL ID : 6dpv.1

Undecorated GDP microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

Oligo State

hetero-6-6-mer

Ligands

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

GTP.1: 21 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, N.228 Chain H: K.252 Ligands: MG.2 21 PLIP interactions: 3 interactions with chain H, 18 interactions with chain A Salt bridges: H:K.252, H:K.252, H:K.252 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: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 GTP.4: 21 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, N.228 Chain I: K.252 Ligands: MG.5 21 PLIP interactions: 18 interactions with chain C, 3 interactions with chain I 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: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: I:K.252, I:K.252, I:K.252 GTP.7: 21 residues within 4Å: Chain E: 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, N.228 Chain G: K.252 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain E, 3 interactions with chain G Hydrogen bonds: E:Q.11, E:A.12, E:Q.15, E:D.98, E:A.99, E:A.100, E:N.101, E:S.140, E:G.144, E:T.145, E:G.146, E:E.183, E:N.206, E:N.206, E:N.228, E:N.228 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: G:K.252, G:K.252, G:K.252 GTP.13: 21 residues within 4Å: Chain F: 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, N.228 Ligands: MG.14 21 PLIP interactions: 18 interactions with chain J, 3 interactions with chain F 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: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: F:K.252, F:K.252, F:K.252 GTP.15: 21 residues within 4Å: Chain B: K.252 Chain K: 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, N.228 Ligands: MG.16 21 PLIP interactions: 18 interactions with chain K, 3 interactions with chain B Hydrogen bonds: K:Q.11, K:A.12, K:Q.15, K:D.98, K:A.99, K:A.100, K:N.101, K:S.140, K:G.144, K:T.145, K:G.146, K:E.183, K:N.206, K:N.206, K:N.228, K:N.228 pi-Stacking: K:Y.224, K:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.17: 21 residues within 4Å: Chain D: 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, N.228 Ligands: MG.18 21 PLIP interactions: 18 interactions with chain L, 3 interactions with chain D 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: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: D:K.252, D:K.252, D:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: Q.11, E.71, D.98 Chain H: K.252 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.98 MG.5: 4 residues within 4Å: Chain C: E.71, D.98 Chain I: K.252 Ligands: GTP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.98 MG.8: 5 residues within 4Å: Chain E: Q.11, E.71, D.98 Chain G: K.252 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.98 MG.14: 6 residues within 4Å: Chain F: K.252 Chain J: Q.11, D.69, E.71, D.98 Ligands: GTP.13 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.98 MG.16: 6 residues within 4Å: Chain B: K.252 Chain K: Q.11, D.69, E.71, D.98 Ligands: GTP.15 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.98 MG.18: 6 residues within 4Å: Chain D: K.252 Chain L: Q.11, D.69, E.71, D.98 Ligands: GTP.17 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.98

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

GDP.3: 14 residues within 4Å: Chain B: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:Q.15, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:D.177, B:D.177, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.6: 14 residues within 4Å: Chain D: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:Q.15, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:D.177, D:D.177, D:E.181, D:N.204, D:N.226, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.9: 14 residues within 4Å: Chain F: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:Q.11, F:Q.11, F:C.12, F:Q.15, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:D.177, F:D.177, F:E.181, F:N.204, F:N.226, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 GDP.10: 14 residues within 4Å: Chain G: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:Q.11, G:C.12, G:Q.15, G:S.138, G:G.142, G:T.143, G:T.143, G:G.144, G:D.177, G:D.177, G:E.181, G:N.204, G:N.226, G:N.226, G:N.226 pi-Stacking: G:Y.222, G:Y.222 GDP.11: 14 residues within 4Å: Chain H: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:Q.15, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:D.177, H:D.177, H:E.181, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GDP.12: 14 residues within 4Å: Chain I: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:Q.11, I:C.12, I:Q.15, I:S.138, I:G.142, I:T.143, I:T.143, I:G.144, I:D.177, I:D.177, I:E.181, I:N.204, I:N.226, I:N.226, I:N.226 pi-Stacking: I:Y.222, I:Y.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, R. et al., Separating the effects of nucleotide and EB binding on microtubule structure. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-07-04

Peptides

Tubulin alpha-1B chain: ACEJKL
Tubulin beta chain: BDFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

J
J

K
K

L
L

B
B

D
D

F
F

G
G

H
H

I
I

Tubulin alpha-1B chain

Tubulin beta chain

Related Entries With Identical Sequence