SMTL ID : 3j6g.1

Minimized average structure of microtubules stabilized by taxol

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-mer

Ligands

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

GTP.1: 18 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 19 PLIP interactions: 16 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.11, A:N.101, 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 Water bridges: A:Q.11, B:K.252, B:K.252 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252 GTP.5: 18 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.6 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.11, C:N.101, 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 Water bridges: C:Q.11, D:K.252, D:K.252 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252 GTP.9: 18 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain F: K.252 Ligands: MG.10 19 PLIP interactions: 16 interactions with chain E, 3 interactions with chain F Hydrogen bonds: E:Q.11, E:N.101, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:G.146, E:E.183, E:N.206, E:N.206, E:N.228, E:N.228 Water bridges: E:Q.11, F:K.252, F:K.252 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: F:K.252 GTP.13: 18 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain H: K.252 Ligands: MG.14 19 PLIP interactions: 16 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:Q.11, G:N.101, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, G:E.183, G:N.206, G:N.206, G:N.228, G:N.228 Water bridges: G:Q.11, H:K.252, H:K.252 pi-Stacking: G:Y.224, G:Y.224 Salt bridges: H:K.252 GTP.17: 18 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain J: K.252 Ligands: MG.18 19 PLIP interactions: 16 interactions with chain I, 3 interactions with chain J Hydrogen bonds: I:Q.11, I:N.101, I:N.101, I:S.140, I:G.144, I:T.145, I:T.145, I:G.146, I:E.183, I:N.206, I:N.206, I:N.228, I:N.228 Water bridges: I:Q.11, J:K.252, J:K.252 pi-Stacking: I:Y.224, I:Y.224 Salt bridges: J:K.252 GTP.21: 18 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain L: K.252 Ligands: MG.22 19 PLIP interactions: 16 interactions with chain K, 3 interactions with chain L Hydrogen bonds: K:Q.11, K:N.101, K:N.101, K:S.140, K:G.144, K:T.145, K:T.145, K:G.146, K:E.183, K:N.206, K:N.206, K:N.228, K:N.228 Water bridges: K:Q.11, L:K.252, L:K.252 pi-Stacking: K:Y.224, K:Y.224 Salt bridges: L:K.252 GTP.25: 18 residues within 4Å: Chain M: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain N: K.252 Ligands: MG.26 19 PLIP interactions: 16 interactions with chain M, 3 interactions with chain N Hydrogen bonds: M:Q.11, M:N.101, M:N.101, M:S.140, M:G.144, M:T.145, M:T.145, M:G.146, M:E.183, M:N.206, M:N.206, M:N.228, M:N.228 Water bridges: M:Q.11, N:K.252, N:K.252 pi-Stacking: M:Y.224, M:Y.224 Salt bridges: N:K.252 GTP.29: 18 residues within 4Å: Chain O: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain P: K.252 Ligands: MG.30 19 PLIP interactions: 16 interactions with chain O, 3 interactions with chain P Hydrogen bonds: O:Q.11, O:N.101, O:N.101, O:S.140, O:G.144, O:T.145, O:T.145, O:G.146, O:E.183, O:N.206, O:N.206, O:N.228, O:N.228 Water bridges: O:Q.11, P:K.252, P:K.252 pi-Stacking: O:Y.224, O:Y.224 Salt bridges: P:K.252 GTP.33: 18 residues within 4Å: Chain Q: G.10, Q.11, A.12, Q.15, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Chain R: K.252 Ligands: MG.34 19 PLIP interactions: 16 interactions with chain Q, 3 interactions with chain R Hydrogen bonds: Q:Q.11, Q:N.101, Q:N.101, Q:S.140, Q:G.144, Q:T.145, Q:T.145, Q:G.146, Q:E.183, Q:N.206, Q:N.206, Q:N.228, Q:N.228 Water bridges: Q:Q.11, R:K.252, R:K.252 pi-Stacking: Q:Y.224, Q:Y.224 Salt bridges: R:K.252

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain B: K.252 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.6: 2 residues within 4Å: Chain D: K.252 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain F: K.252 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Chain H: K.252 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain J: K.252 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain L: K.252 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain N: K.252 Ligands: GTP.25 No protein-ligand interaction detected (PLIP) MG.30: 2 residues within 4Å: Chain P: K.252 Ligands: GTP.29 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain R: K.252 Ligands: GTP.33 No protein-ligand interaction detected (PLIP)

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

GDP.3: 15 residues within 4Å: Chain B: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:N.99, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222 GDP.7: 15 residues within 4Å: Chain D: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:N.99, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.226, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.11: 15 residues within 4Å: Chain F: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:N.99, F:N.99, F:S.138, F:G.142, F:T.143, F:T.143, F:T.143, F:G.144, F:E.181, F:N.204, F:N.226, F:N.226, F:N.226 pi-Stacking: F:Y.222, F:Y.222 GDP.15: 15 residues within 4Å: Chain H: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, 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:N.99, H:N.99, H:S.138, H:G.142, H:T.143, H:T.143, H:T.143, H:G.144, H:E.181, H:N.204, H:N.226, H:N.226, H:N.226 pi-Stacking: H:Y.222, H:Y.222 GDP.19: 15 residues within 4Å: Chain J: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:N.99, J:N.99, J:S.138, J:G.142, J:T.143, J:T.143, J:T.143, J:G.144, J:E.181, J:N.204, J:N.226, J:N.226, J:N.226 pi-Stacking: J:Y.222, J:Y.222 GDP.23: 15 residues within 4Å: Chain L: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:N.99, L:N.99, L:S.138, L:G.142, L:T.143, L:T.143, L:T.143, L:G.144, L:E.181, L:N.204, L:N.226, L:N.226, L:N.226 pi-Stacking: L:Y.222, L:Y.222 GDP.27: 15 residues within 4Å: Chain N: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:N.99, N:N.99, N:S.138, N:G.142, N:T.143, N:T.143, N:T.143, N:G.144, N:E.181, N:N.204, N:N.226, N:N.226, N:N.226 pi-Stacking: N:Y.222, N:Y.222 GDP.31: 15 residues within 4Å: Chain P: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain P Hydrogen bonds: P:Q.11, P:C.12, P:N.99, P:N.99, P:S.138, P:G.142, P:T.143, P:T.143, P:T.143, P:G.144, P:E.181, P:N.204, P:N.226, P:N.226, P:N.226 pi-Stacking: P:Y.222, P:Y.222 GDP.35: 15 residues within 4Å: Chain R: Q.11, C.12, Q.15, N.99, S.138, G.141, G.142, T.143, G.144, V.169, V.175, E.181, N.204, Y.222, N.226 17 PLIP interactions: 17 interactions with chain R Hydrogen bonds: R:Q.11, R:C.12, R:N.99, R:N.99, R:S.138, R:G.142, R:T.143, R:T.143, R:T.143, R:G.144, R:E.181, R:N.204, R:N.226, R:N.226, R:N.226 pi-Stacking: R:Y.222, R:Y.222

9 x TA1: TAXOL(Non-covalent)

TA1.4: 13 residues within 4Å: Chain B: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.23, B:V.23, B:D.26, B:H.227, B:L.228, B:F.270, B:T.274, B:L.361, B:L.361 Hydrogen bonds: B:T.274, B:Q.279, B:R.359, B:R.359 pi-Stacking: B:H.227 TA1.8: 13 residues within 4Å: Chain D: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.23, D:V.23, D:D.26, D:H.227, D:L.228, D:F.270, D:T.274, D:L.361, D:L.361 Hydrogen bonds: D:T.274, D:Q.279, D:R.359, D:R.359 pi-Stacking: D:H.227 TA1.12: 13 residues within 4Å: Chain F: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:V.23, F:V.23, F:D.26, F:H.227, F:L.228, F:F.270, F:T.274, F:L.361, F:L.361 Hydrogen bonds: F:T.274, F:Q.279, F:R.359, F:R.359 pi-Stacking: F:H.227 TA1.16: 13 residues within 4Å: Chain H: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:V.23, H:V.23, H:D.26, H:H.227, H:L.228, H:F.270, H:T.274, H:L.361, H:L.361 Hydrogen bonds: H:T.274, H:Q.279, H:R.359, H:R.359 pi-Stacking: H:H.227 TA1.20: 13 residues within 4Å: Chain J: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:V.23, J:V.23, J:D.26, J:H.227, J:L.228, J:F.270, J:T.274, J:L.361, J:L.361 Hydrogen bonds: J:T.274, J:Q.279, J:R.359, J:R.359 pi-Stacking: J:H.227 TA1.24: 13 residues within 4Å: Chain L: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:V.23, L:V.23, L:D.26, L:H.227, L:L.228, L:F.270, L:T.274, L:L.361, L:L.361 Hydrogen bonds: L:T.274, L:Q.279, L:R.359, L:R.359 pi-Stacking: L:H.227 TA1.28: 13 residues within 4Å: Chain N: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain N Hydrophobic interactions: N:V.23, N:V.23, N:D.26, N:H.227, N:L.228, N:F.270, N:T.274, N:L.361, N:L.361 Hydrogen bonds: N:T.274, N:Q.279, N:R.359, N:R.359 pi-Stacking: N:H.227 TA1.32: 13 residues within 4Å: Chain P: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain P Hydrophobic interactions: P:V.23, P:V.23, P:D.26, P:H.227, P:L.228, P:F.270, P:T.274, P:L.361, P:L.361 Hydrogen bonds: P:T.274, P:Q.279, P:R.359, P:R.359 pi-Stacking: P:H.227 TA1.36: 13 residues within 4Å: Chain R: V.23, D.26, D.224, H.227, L.228, A.231, S.234, F.270, P.272, T.274, Q.279, R.359, L.361 14 PLIP interactions: 14 interactions with chain R Hydrophobic interactions: R:V.23, R:V.23, R:D.26, R:H.227, R:L.228, R:F.270, R:T.274, R:L.361, R:L.361 Hydrogen bonds: R:T.274, R:Q.279, R:R.359, R:R.359 pi-Stacking: R:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alushin, G.M. et al., High-Resolution Microtubule Structures Reveal the Structural Transitions in alpha beta-Tubulin upon GTP Hydrolysis. Cell(Cambridge,Mass.) (2014)

Release Date

2014-06-04

Peptides

Tubulin alpha-1A chain: ACEGIKMOQ
Tubulin beta chain: BDFHJLNPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

Tubulin alpha-1A chain

Tubulin beta chain

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