SMTL ID : 5jco.1

Structure and dynamics of single-isoform recombinant neuronal human tubulin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.00 Å

Oligo State

hetero-6-6-mer

Ligands

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

G2P.1: 21 residues within 4Å: Chain A: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, N.226 Ligands: MG.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.11, A:C.12, A:Q.15, A:G.98, A:N.99, A:S.138, A:G.142, A:T.143, A:G.144, A:N.204, A:N.226, A:N.226, A:N.226 G2P.5: 21 residues within 4Å: Chain C: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, N.226 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:Q.11, C:C.12, C:Q.15, C:G.98, C:N.99, C:S.138, C:G.142, C:T.143, C:G.144, C:N.204, C:Y.222, C:N.226, C:N.226, C:N.226 pi-Stacking: C:Y.222 G2P.9: 21 residues within 4Å: Chain E: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, N.226 Ligands: MG.10 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:Q.11, E:C.12, E:Q.15, E:A.97, E:G.98, E:N.99, E:S.138, E:G.142, E:T.143, E:G.144, E:N.204, E:N.226, E:N.226, E:N.226 G2P.11: 20 residues within 4Å: Chain F: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, E.181, N.204, Y.222, N.226 Ligands: MG.12 15 PLIP interactions: 15 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:G.144, F:N.204, F:N.226, F:N.226, F:N.226 pi-Stacking: F:Y.222 G2P.13: 21 residues within 4Å: Chain G: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, N.226 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:Q.11, G:C.12, G:Q.15, G:A.97, G:G.98, G:N.99, G:S.138, G:G.142, G:T.143, G:G.144, G:N.204, G:N.226, G:N.226, G:N.226 G2P.21: 21 residues within 4Å: Chain K: G.10, Q.11, C.12, Q.15, E.69, A.97, G.98, N.99, S.138, G.141, G.142, T.143, G.144, V.169, D.177, T.178, E.181, N.204, Y.222, N.226 Ligands: MG.22 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:Q.11, K:C.12, K:Q.15, K:G.98, K:N.99, K:S.138, K:G.142, K:T.143, K:G.144, K:N.204, K:N.226, K:N.226, K:N.226 pi-Stacking: K:Y.222

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.69 Ligands: G2P.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: Q.11, E.71 Ligands: GTP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: Q.11, E.69 Ligands: G2P.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain D: Q.11, E.71 Ligands: GTP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain E: Q.11, E.69 Ligands: G2P.9 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain F: Q.11, E.69 Ligands: G2P.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain G: Q.11, E.69 Ligands: G2P.13 No protein-ligand interaction detected (PLIP) MG.16: 3 residues within 4Å: Chain H: Q.11, E.71 Ligands: GTP.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain I: Q.11, E.71 Ligands: GTP.17 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain J: Q.11, E.71 Ligands: GTP.19 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain K: Q.11, E.69 Ligands: G2P.21 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain L: Q.11, E.71 Ligands: GTP.23 No protein-ligand interaction detected (PLIP)

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

GTP.3: 20 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, D.98, A.99, 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.4 19 PLIP interactions: 1 interactions with chain G, 18 interactions with chain B Salt bridges: G:K.252 Hydrogen bonds: B:Q.11, B:Q.11, B:A.12, B:Q.15, B:N.101, B:N.101, B:S.140, B:G.144, B:T.145, B:G.146, B:E.183, B:N.206, B:N.206, B:Y.224, B:N.228, B:N.228 pi-Stacking: B:Y.224, B:Y.224 GTP.7: 20 residues within 4Å: Chain D: G.10, Q.11, A.12, Q.15, D.98, A.99, 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 F: K.252 Ligands: MG.8 19 PLIP interactions: 18 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Q.11, D:Q.11, D:A.12, D:Q.15, D:N.101, D:N.101, D:S.140, D:G.144, D:T.145, D:G.146, D:E.183, D:N.206, D:N.206, D:Y.224, D:N.228, D:N.228 pi-Stacking: D:Y.224, D:Y.224 Salt bridges: F:K.252 GTP.15: 20 residues within 4Å: Chain H: G.10, Q.11, A.12, Q.15, D.98, A.99, 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 K: K.252 Ligands: MG.16 19 PLIP interactions: 18 interactions with chain H, 1 interactions with chain K Hydrogen bonds: H:Q.11, H:Q.11, H:A.12, H:Q.15, H:N.101, H:N.101, H:S.140, H:G.144, H:T.145, H:G.146, H:E.183, H:N.206, H:N.206, H:Y.224, H:N.228, H:N.228 pi-Stacking: H:Y.224, H:Y.224 Salt bridges: K:K.252 GTP.17: 20 residues within 4Å: Chain C: K.252 Chain I: G.10, Q.11, A.12, Q.15, D.98, A.99, 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 18 PLIP interactions: 17 interactions with chain I, 1 interactions with chain C Hydrogen bonds: I:Q.11, I:Q.11, I:A.12, I:Q.15, I:N.101, I:S.140, I:G.144, I:T.145, I:G.146, I:E.183, I:N.206, I:N.206, I:Y.224, I:N.228, I:N.228 pi-Stacking: I:Y.224, I:Y.224 Salt bridges: C:K.252 GTP.19: 20 residues within 4Å: Chain A: K.252 Chain J: G.10, Q.11, A.12, Q.15, D.98, A.99, 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.20 18 PLIP interactions: 17 interactions with chain J, 1 interactions with chain A Hydrogen bonds: J:Q.11, J:Q.11, J:A.12, J:Q.15, 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:Y.224, J:N.228, J:N.228 pi-Stacking: J:Y.224, J:Y.224 Salt bridges: A:K.252 GTP.23: 20 residues within 4Å: Chain E: K.252 Chain L: G.10, Q.11, A.12, Q.15, D.98, A.99, 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.24 19 PLIP interactions: 18 interactions with chain L, 1 interactions with chain E Hydrogen bonds: L:Q.11, L:Q.11, L:A.12, L:Q.15, L:N.101, 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:Y.224, L:N.228, L:N.228 pi-Stacking: L:Y.224, L:Y.224 Salt bridges: E:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vemu, A. et al., Structure and Dynamics of Single-isoform Recombinant Neuronal Human Tubulin. J.Biol.Chem. (2016)

Release Date

2016-05-04

Peptides

Tubulin beta-3 chain: ACEFGK
Tubulin alpha-1A chain: BDHIJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
I

E
J

F
C

G
D

K
L

B
H

D
E

H
F

I
A

J
B

L
G

Tubulin beta-3 chain

Tubulin alpha-1A chain

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