SMTL ID : 3j6e.1

Energy minimized average structure of Microtubules stabilized by GmpCpp

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-9-9-mer

Ligands

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

GTP.1: 20 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain B: K.252 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:A.12, A:A.99, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:T.145, A:G.146, A:N.206, A:N.228, A:N.228, A:N.228 Water bridges: A:Q.11, A:D.98 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252 GTP.5: 20 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Q.11, C:A.12, C:A.99, C:N.101, C:N.101, C:S.140, C:G.144, C:T.145, C:T.145, C:G.146, C:N.206, C:N.228, C:N.228, C:N.228 Water bridges: C:Q.11, C:D.98 pi-Stacking: C:Y.224, C:Y.224 Salt bridges: D:K.252, D:K.252 GTP.9: 20 residues within 4Å: Chain E: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain F: K.252 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.11, E:A.12, E:A.99, E:N.101, E:N.101, E:S.140, E:G.144, E:T.145, E:T.145, E:G.146, E:N.206, E:N.228, E:N.228, E:N.228 Water bridges: E:Q.11, E:D.98 pi-Stacking: E:Y.224, E:Y.224 Salt bridges: F:K.252, F:K.252 GTP.13: 20 residues within 4Å: Chain G: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain H: K.252 Ligands: MG.14 20 PLIP interactions: 18 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Q.11, G:A.12, G:A.99, G:N.101, G:N.101, G:S.140, G:G.144, G:T.145, G:T.145, G:G.146, G:N.206, G:N.228, G:N.228, G:N.228 Water bridges: G:Q.11, G:D.98 pi-Stacking: G:Y.224, G:Y.224 Salt bridges: H:K.252, H:K.252 GTP.17: 20 residues within 4Å: Chain I: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain J: K.252 Ligands: MG.18 20 PLIP interactions: 18 interactions with chain I, 2 interactions with chain J Hydrogen bonds: I:Q.11, I:A.12, I:A.99, I:N.101, I:N.101, I:S.140, I:G.144, I:T.145, I:T.145, I:G.146, I:N.206, I:N.228, I:N.228, I:N.228 Water bridges: I:Q.11, I:D.98 pi-Stacking: I:Y.224, I:Y.224 Salt bridges: J:K.252, J:K.252 GTP.21: 20 residues within 4Å: Chain K: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain L: K.252 Ligands: MG.22 20 PLIP interactions: 18 interactions with chain K, 2 interactions with chain L Hydrogen bonds: K:Q.11, K:A.12, K:A.99, K:N.101, K:N.101, K:S.140, K:G.144, K:T.145, K:T.145, K:G.146, K:N.206, K:N.228, K:N.228, K:N.228 Water bridges: K:Q.11, K:D.98 pi-Stacking: K:Y.224, K:Y.224 Salt bridges: L:K.252, L:K.252 GTP.25: 20 residues within 4Å: Chain M: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain N: K.252 Ligands: MG.26 20 PLIP interactions: 18 interactions with chain M, 2 interactions with chain N Hydrogen bonds: M:Q.11, M:A.12, M:A.99, M:N.101, M:N.101, M:S.140, M:G.144, M:T.145, M:T.145, M:G.146, M:N.206, M:N.228, M:N.228, M:N.228 Water bridges: M:Q.11, M:D.98 pi-Stacking: M:Y.224, M:Y.224 Salt bridges: N:K.252, N:K.252 GTP.29: 20 residues within 4Å: Chain O: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain P: K.252 Ligands: MG.30 20 PLIP interactions: 18 interactions with chain O, 2 interactions with chain P Hydrogen bonds: O:Q.11, O:A.12, O:A.99, O:N.101, O:N.101, O:S.140, O:G.144, O:T.145, O:T.145, O:G.146, O:N.206, O:N.228, O:N.228, O:N.228 Water bridges: O:Q.11, O:D.98 pi-Stacking: O:Y.224, O:Y.224 Salt bridges: P:K.252, P:K.252 GTP.33: 20 residues within 4Å: Chain Q: G.10, Q.11, A.12, Q.15, I.16, D.98, A.99, N.101, S.140, G.143, G.144, T.145, G.146, V.177, N.206, Y.224, N.228, I.231 Chain R: K.252 Ligands: MG.34 20 PLIP interactions: 18 interactions with chain Q, 2 interactions with chain R Hydrogen bonds: Q:Q.11, Q:A.12, Q:A.99, Q:N.101, Q:N.101, Q:S.140, Q:G.144, Q:T.145, Q:T.145, Q:G.146, Q:N.206, Q:N.228, Q:N.228, Q:N.228 Water bridges: Q:Q.11, Q:D.98 pi-Stacking: Q:Y.224, Q:Y.224 Salt bridges: R:K.252, R:K.252

18 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, D.69 Ligands: GTP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: D.67, E.69 Ligands: G2P.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.11, D.69 Ligands: GTP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: D.67, E.69 Ligands: G2P.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.11, D.69 Ligands: GTP.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: D.67, E.69 Ligands: G2P.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: Q.11, D.69 Ligands: GTP.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: D.67, E.69 Ligands: G2P.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain I: Q.11, D.69 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: D.67, E.69 Ligands: G2P.19 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain K: Q.11, D.69 Ligands: GTP.21 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain L: D.67, E.69 Ligands: G2P.23 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain M: Q.11, D.69 Ligands: GTP.25 No protein-ligand interaction detected (PLIP) MG.28: 3 residues within 4Å: Chain N: D.67, E.69 Ligands: G2P.27 No protein-ligand interaction detected (PLIP) MG.30: 3 residues within 4Å: Chain O: Q.11, D.69 Ligands: GTP.29 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain P: D.67, E.69 Ligands: G2P.31 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain Q: Q.11, D.69 Ligands: GTP.33 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain R: D.67, E.69 Ligands: G2P.35 No protein-ligand interaction detected (PLIP)

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

G2P.3: 19 residues within 4Å: Chain B: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.4 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:Q.15, B:A.97, B:G.98, B:N.99, B:S.138, B:G.142, B:T.143, B:T.143, B:G.144, B:E.181, B:N.204, B:N.226, B:N.226, B:N.226 Water bridges: B:L.68, B:T.143 pi-Stacking: B:Y.222, B:Y.222 G2P.7: 19 residues within 4Å: Chain D: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.8 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:Q.11, D:C.12, D:Q.15, D:A.97, D:G.98, D:N.99, D:S.138, D:G.142, D:T.143, D:T.143, D:G.144, D:E.181, D:N.204, D:N.226, D:N.226, D:N.226 Water bridges: D:L.68, D:T.143 pi-Stacking: D:Y.222, D:Y.222 G2P.11: 19 residues within 4Å: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.12 20 PLIP interactions: 20 interactions with chain F Hydrogen bonds: F:Q.11, F:C.12, F:Q.15, F:A.97, F:G.98, F:N.99, F:S.138, F:G.142, F:T.143, F:T.143, F:G.144, F:E.181, F:N.204, F:N.226, F:N.226, F:N.226 Water bridges: F:L.68, F:T.143 pi-Stacking: F:Y.222, F:Y.222 G2P.15: 19 residues within 4Å: Chain H: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.16 20 PLIP interactions: 20 interactions with chain H Hydrogen bonds: H:Q.11, H:C.12, H:Q.15, H:A.97, H:G.98, H:N.99, H:S.138, H:G.142, H:T.143, H:T.143, H:G.144, H:E.181, H:N.204, H:N.226, H:N.226, H:N.226 Water bridges: H:L.68, H:T.143 pi-Stacking: H:Y.222, H:Y.222 G2P.19: 19 residues within 4Å: 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, G.144, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.20 20 PLIP interactions: 20 interactions with chain J Hydrogen bonds: J:Q.11, J:C.12, J:Q.15, J:A.97, J:G.98, J:N.99, J:S.138, J:G.142, J:T.143, J:T.143, J:G.144, J:E.181, J:N.204, J:N.226, J:N.226, J:N.226 Water bridges: J:L.68, J:T.143 pi-Stacking: J:Y.222, J:Y.222 G2P.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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.24 20 PLIP interactions: 20 interactions with chain L Hydrogen bonds: L:Q.11, L:C.12, L:Q.15, L:A.97, L:G.98, L:N.99, L:S.138, L:G.142, L:T.143, L:T.143, L:G.144, L:E.181, L:N.204, L:N.226, L:N.226, L:N.226 Water bridges: L:L.68, L:T.143 pi-Stacking: L:Y.222, L:Y.222 G2P.27: 19 residues within 4Å: Chain N: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.28 20 PLIP interactions: 20 interactions with chain N Hydrogen bonds: N:Q.11, N:C.12, N:Q.15, N:A.97, N:G.98, N:N.99, N:S.138, N:G.142, N:T.143, N:T.143, N:G.144, N:E.181, N:N.204, N:N.226, N:N.226, N:N.226 Water bridges: N:L.68, N:T.143 pi-Stacking: N:Y.222, N:Y.222 G2P.31: 19 residues within 4Å: Chain P: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.32 20 PLIP interactions: 20 interactions with chain P Hydrogen bonds: P:Q.11, P:C.12, P:Q.15, P:A.97, P:G.98, P:N.99, P:S.138, P:G.142, P:T.143, P:T.143, P:G.144, P:E.181, P:N.204, P:N.226, P:N.226, P:N.226 Water bridges: P:L.68, P:T.143 pi-Stacking: P:Y.222, P:Y.222 G2P.35: 19 residues within 4Å: Chain R: 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, V.169, E.181, N.204, Y.222, N.226 Ligands: MG.36 20 PLIP interactions: 20 interactions with chain R Hydrogen bonds: R:Q.11, R:C.12, R:Q.15, R:A.97, R:G.98, R:N.99, R:S.138, R:G.142, R:T.143, R:T.143, R:G.144, R:E.181, R:N.204, R:N.226, R:N.226, R:N.226 Water bridges: R:L.68, R:T.143 pi-Stacking: R:Y.222, R:Y.222

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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