SMTL ID : 9g0r.1

Xenopus laevis undecorated microtubule - 15 protofilament, 4-start helix

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GDP.1: 20 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:N.99, A:S.138, A:G.142, A:T.143, A:G.144, A:N.204, A:N.204, A:N.204, A:Y.222, A:N.226, A:N.226, A:N.226 GDP.2: 20 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:N.204, B:N.204, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226 GDP.3: 20 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.11, C:C.12, C:N.99, C:S.138, C:G.142, C:T.143, C:G.144, C:N.204, C:N.204, C:N.204, C:Y.222, C:N.226, C:N.226, C:N.226 GDP.4: 21 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 Chain G: L.247 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:N.204, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226, D:N.226 GDP.5: 21 residues within 4Å: Chain E: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 Chain H: L.247 14 PLIP interactions: 14 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:G.144, E:N.204, E:N.204, E:N.204, E:Y.222, E:N.226, E:N.226, E:N.226 GDP.6: 21 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, I.16, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, L.225, N.226 Chain I: L.247 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:N.99, F:S.138, F:G.142, F:T.143, F:G.144, F:N.204, F:N.204, F:N.204, F:Y.222, F:N.226, F:N.226, F:N.226

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

GTP.7: 26 residues within 4Å: Chain A: L.246, K.252 Chain G: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.8 27 PLIP interactions: 24 interactions with chain G, 3 interactions with chain A Hydrogen bonds: G:Q.11, G:A.12, G:Q.15, G:A.98, G:A.99, G:N.100, G:N.100, G:S.139, G:G.142, G:T.144, G:T.144, G:T.144, G:G.145, G:T.178, G:T.178, G:N.205, G:N.205, G:N.205, G:Y.223, G:N.227, G:N.227, G:N.227 pi-Stacking: G:Y.223, G:Y.223 Salt bridges: A:K.252, A:K.252, A:K.252 GTP.9: 26 residues within 4Å: Chain B: L.246, K.252 Chain H: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.10 27 PLIP interactions: 24 interactions with chain H, 3 interactions with chain B Hydrogen bonds: H:Q.11, H:A.12, H:Q.15, H:A.98, H:A.99, H:N.100, H:N.100, H:S.139, H:G.142, H:T.144, H:T.144, H:T.144, H:G.145, H:T.178, H:T.178, H:N.205, H:N.205, H:N.205, H:Y.223, H:N.227, H:N.227, H:N.227 pi-Stacking: H:Y.223, H:Y.223 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.11: 26 residues within 4Å: Chain C: L.246, K.252 Chain I: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.12 27 PLIP interactions: 24 interactions with chain I, 3 interactions with chain C Hydrogen bonds: I:Q.11, I:A.12, I:Q.15, I:A.98, I:A.99, I:N.100, I:N.100, I:S.139, I:G.142, I:T.144, I:T.144, I:T.144, I:G.145, I:T.178, I:T.178, I:N.205, I:N.205, I:N.205, I:Y.223, I:N.227, I:N.227, I:N.227 pi-Stacking: I:Y.223, I:Y.223 Salt bridges: C:K.252, C:K.252, C:K.252 GTP.13: 26 residues within 4Å: Chain D: L.246, K.252 Chain J: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.14 27 PLIP interactions: 24 interactions with chain J, 3 interactions with chain D Hydrogen bonds: J:Q.11, J:A.12, J:Q.15, J:A.98, J:A.99, J:N.100, J:N.100, J:S.139, J:G.142, J:T.144, J:T.144, J:T.144, J:G.145, J:T.178, J:T.178, J:N.205, J:N.205, J:N.205, J:Y.223, J:N.227, J:N.227, J:N.227 pi-Stacking: J:Y.223, J:Y.223 Salt bridges: D:K.252, D:K.252, D:K.252 GTP.15: 26 residues within 4Å: Chain E: L.246, K.252 Chain K: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.16 27 PLIP interactions: 24 interactions with chain K, 3 interactions with chain E Hydrogen bonds: K:Q.11, K:A.12, K:Q.15, K:A.98, K:A.99, K:N.100, K:N.100, K:S.139, K:G.142, K:T.144, K:T.144, K:T.144, K:G.145, K:T.178, K:T.178, K:N.205, K:N.205, K:N.205, K:Y.223, K:N.227, K:N.227, K:N.227 pi-Stacking: K:Y.223, K:Y.223 Salt bridges: E:K.252, E:K.252, E:K.252 GTP.17: 26 residues within 4Å: Chain F: L.246, K.252 Chain L: G.10, Q.11, A.12, Q.15, M.16, D.97, A.98, A.99, N.100, S.139, G.141, G.142, G.143, T.144, G.145, V.170, T.178, E.182, N.205, Y.223, L.226, N.227, I.230 Ligands: MG.18 27 PLIP interactions: 24 interactions with chain L, 3 interactions with chain F Hydrogen bonds: L:Q.11, L:A.12, L:Q.15, L:A.98, L:A.99, L:N.100, L:N.100, L:S.139, L:G.142, L:T.144, L:T.144, L:T.144, L:G.145, L:T.178, L:T.178, L:N.205, L:N.205, L:N.205, L:Y.223, L:N.227, L:N.227, L:N.227 pi-Stacking: L:Y.223, L:Y.223 Salt bridges: F:K.252, F:K.252, F:K.252

6 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain G: Q.11, E.70, D.97 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:E.70 MG.10: 4 residues within 4Å: Chain H: Q.11, E.70, D.97 Ligands: GTP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.70 MG.12: 4 residues within 4Å: Chain I: Q.11, E.70, D.97 Ligands: GTP.11 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:E.70 MG.14: 4 residues within 4Å: Chain J: Q.11, E.70, D.97 Ligands: GTP.13 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.70 MG.16: 4 residues within 4Å: Chain K: Q.11, E.70, D.97 Ligands: GTP.15 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.70 MG.18: 4 residues within 4Å: Chain L: Q.11, E.70, D.97 Ligands: GTP.17 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:E.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Troman, L. et al., Mechanistic basis of temperature adaptation in microtubule dynamics across frog species. Curr.Biol. (2025)

Release Date

2025-01-15

Peptides

Tubulin beta-4 chain: ABCDEF
Tubulin alpha chain: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
a

H
b

I
c

J
d

K
e

L
f

Tubulin beta-4 chain

Tubulin alpha chain

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