SMTL ID : 6qve.1

NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-2-mer

Ligands

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

GTP.1: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, E.71, D.98, A.100, N.101, S.140, G.142, G.143, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain E: L.246, K.252 Ligands: MG.2 19 PLIP interactions: 2 interactions with chain E, 17 interactions with chain A Salt bridges: E:K.252, E:K.252 Hydrogen bonds: A:Q.11, A:A.12, A:D.98, A:A.100, A:N.101, A:S.140, A:G.143, A:T.145, A:T.145, A:T.145, A:G.146, A:E.183, A:N.206, A:N.228, A:N.228, A:N.228 pi-Cation interactions: A:Y.224 GTP.3: 23 residues within 4Å: Chain B: G.10, Q.11, A.12, Q.15, I.16, E.71, D.98, A.100, N.101, S.140, G.143, T.145, G.146, I.171, T.179, E.183, N.206, Y.224, N.228 Chain D: Q.245, L.246, K.252 Ligands: MG.4 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Q.11, B:A.12, B:A.100, B:N.101, B:S.140, B:G.143, B:T.145, B:T.145, B:T.145, B:G.146, B:E.183, B:N.206, B:N.228, B:N.228, B:N.228 pi-Cation interactions: B:Y.224 Salt bridges: D:K.252, D:K.252

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.69, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.4: 3 residues within 4Å: Chain B: E.71 Chain D: K.252 Ligands: GTP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.71

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

GDP.5: 11 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, G.144, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:N.204, D:N.204, D:Y.222, D:N.226, D:N.226 pi-Stacking: D:Y.222, D:Y.222 GDP.7: 11 residues within 4Å: Chain E: G.10, Q.11, C.12, Q.15, G.141, G.142, T.143, G.144, N.204, Y.222, N.226 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Q.11, E:Q.11, E:C.12, E:G.141, E:G.142, E:T.143, E:T.143, E:T.143, E:G.144, E:N.204, E:N.204, E:Y.222, E:N.226, E:N.226 pi-Stacking: E:Y.222, E:Y.222

2 x TA1: TAXOL(Non-covalent)

TA1.6: 15 residues within 4Å: Chain D: E.22, V.23, D.26, E.27, D.224, H.227, A.231, S.234, T.274, R.276, Q.279, P.358, R.359, G.360, L.361 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:E.22, D:V.23, D:A.231, D:L.361 Hydrogen bonds: D:T.274, D:R.276, D:R.359, D:R.359 Salt bridges: D:R.276 pi-Cation interactions: D:K.19, D:H.227 TA1.8: 15 residues within 4Å: Chain E: E.22, V.23, D.26, E.27, D.224, H.227, A.231, S.234, T.274, R.276, Q.279, P.358, R.359, G.360, L.361 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:V.23, E:A.231, E:P.358, E:L.361 Hydrogen bonds: E:T.274, E:R.359, E:R.359 Salt bridges: E:R.276 pi-Cation interactions: E:K.19, E:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Atherton, J. et al., Structural determinants of microtubule minus end preference in CAMSAP CKK domains. Nat Commun (2019)

Release Date

2019-11-27

Peptides

Tubulin alpha-1B chain: AB
Predicted protein: C
Beta1-tubulin: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
W

D
H

E
G

Tubulin alpha-1B chain

Predicted protein

Beta1-tubulin

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