SMTL ID : 9f3b.1

Undecorated 13pf E254Q microtubule from recombinant human tubulin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

GTP.1: 21 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.83, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, L.239, N.240 Chain D: K.252 Ligands: MG.2 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.11, A:A.12, A:A.111, A:A.112, A:N.113, A:N.113, A:S.152, A:G.155, A:G.156, A:T.157, A:E.195, A:N.218, A:N.218, A:N.240, A:N.240 pi-Stacking: A:Y.236, A:Y.236 Salt bridges: D:K.252, D:K.252 GTP.3: 22 residues within 4Å: Chain A: N.261, Q.266 Chain B: G.10, Q.11, C.12, Q.15, E.69, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, 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:G.98, B:N.99, B:N.99, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:D.177, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222 GTP.5: 20 residues within 4Å: Chain B: K.252 Chain C: G.10, Q.11, A.12, Q.15, E.83, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, N.240 Ligands: MG.6 20 PLIP interactions: 17 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Q.11, C:A.12, C:A.111, C:A.112, C:N.113, C:S.152, C:G.155, C:G.156, C:T.157, C:G.158, C:T.191, C:E.195, C:N.218, C:N.240, C:N.240, C:N.240 pi-Stacking: C:Y.236 Salt bridges: B:K.252, B:K.252, B:K.252 GTP.7: 18 residues within 4Å: Chain D: Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, N.204, Y.222, L.225, N.226 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:G.98, D:N.99, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:G.144, D:N.204, D:N.226, D:N.226, D:N.226 pi-Stacking: D:Y.222 GTP.9: 20 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, L.239, N.240 Chain H: K.252 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain H Hydrogen bonds: E:Q.11, E:A.12, E:D.110, E:A.111, E:A.112, E:N.113, E:S.152, E:G.155, E:G.156, E:T.157, E:T.191, E:E.195, E:E.195, E:N.218, E:N.218, E:N.240, E:N.240 pi-Cation interactions: E:Y.236 Salt bridges: H:K.252, H:K.252 GTP.11: 19 residues within 4Å: Chain E: Q.266 Chain F: G.10, Q.11, C.12, Q.15, G.96, 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.12 19 PLIP interactions: 16 interactions with chain F, 3 interactions with chain E Hydrogen bonds: F:Q.11, F:C.12, F:A.97, F:G.98, F:N.99, F:S.138, F:G.141, F:G.142, F:T.143, F:G.144, F:D.177, F:D.177, F:N.204, F:N.226, F:N.226, F:N.226, E:Q.266, E:Q.266, E:Q.266 GTP.13: 21 residues within 4Å: Chain F: K.252 Chain G: G.10, Q.11, A.12, Q.15, E.83, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, L.239, N.240 Ligands: MG.14 18 PLIP interactions: 15 interactions with chain G, 3 interactions with chain F Hydrogen bonds: G:Q.11, G:A.12, G:A.111, G:A.112, G:N.113, G:S.152, G:G.156, G:T.157, G:E.195, G:E.195, G:N.218, G:N.240, G:N.240, G:N.240 pi-Stacking: G:Y.236 Salt bridges: F:K.252, F:K.252, F:K.252 GTP.15: 19 residues within 4Å: Chain H: G.10, Q.11, C.12, Q.15, E.69, G.96, 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.16 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:G.98, H:N.99, H:N.99, H:S.138, H:G.141, H:G.142, H:T.143, H:G.144, H:N.204, H:N.226, H:N.226, H:N.226 GTP.17: 20 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, L.239, N.240 Chain L: K.252 Ligands: MG.18 19 PLIP interactions: 17 interactions with chain I, 2 interactions with chain L Hydrogen bonds: I:Q.11, I:A.12, I:A.111, I:A.112, I:N.113, I:S.152, I:G.155, I:G.156, I:T.157, I:E.195, I:E.195, I:N.218, I:N.240, I:N.240, I:N.240 pi-Stacking: I:Y.236 pi-Cation interactions: I:Y.236 Salt bridges: L:K.252, L:K.252 GTP.19: 18 residues within 4Å: Chain I: Q.266 Chain J: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, D.177, N.204, Y.222, N.226 Ligands: MG.20 18 PLIP interactions: 18 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:A.97, J:G.98, J:N.99, J:N.99, J:S.138, J:G.141, J:G.142, J:T.143, J:G.144, J:D.177, J:D.177, J:N.204, J:N.226, J:N.226, J:N.226 pi-Stacking: J:Y.222 GTP.21: 19 residues within 4Å: Chain J: K.252 Chain K: G.10, Q.11, A.12, Q.15, D.110, A.111, A.112, N.113, S.152, G.155, G.156, T.157, T.191, E.195, N.218, Y.236, N.240 Ligands: MG.22 18 PLIP interactions: 16 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:Q.11, K:A.12, K:A.111, K:A.112, K:N.113, K:S.152, K:G.156, K:T.157, K:E.195, K:E.195, K:N.218, K:N.240, K:N.240, K:N.240 pi-Stacking: K:Y.236, K:Y.236 Salt bridges: J:K.252, J:K.252 GTP.23: 19 residues within 4Å: Chain L: G.10, Q.11, C.12, Q.15, G.96, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, D.177, T.178, N.204, Y.222, N.226 Ligands: MG.24 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:G.98, L:N.99, L:N.99, L:S.138, L:G.141, L:G.142, L:T.143, L:G.144, L:N.204, L:N.226, L:N.226, L:N.226 pi-Stacking: L:Y.222

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.83 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.83 MG.4: 3 residues within 4Å: Chain B: D.67, E.69 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.69 MG.6: 3 residues within 4Å: Chain C: E.83, D.110 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: D.67, E.69, T.143 Ligands: GTP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:E.69 MG.10: 3 residues within 4Å: Chain E: E.83, D.110 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: E.69 Ligands: GTP.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: E.83, D.110 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain H: E.69 Ligands: GTP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.69 MG.18: 3 residues within 4Å: Chain I: E.83, D.110 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain J: E.69 Ligands: GTP.19 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain J: K.252 Chain K: D.110, T.157 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain L: E.69 Ligands: GTP.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Estevez-Gallego, J. et al., Hydrolysis-deficient mosaic microtubules as faithful mimics of the GTP cap. Nat Commun (2025)

Release Date

2025-03-19

Peptides

Detyrosinated tubulin alpha-1B chain: ACEGIK
Tubulin beta-3 chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
G

E
C

G
I

I
E

K
K

B
B

D
N

F
D

H
P

J
F

L
R

Detyrosinated tubulin alpha-1B chain

Tubulin beta-3 chain

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