SMTL ID : 6bbn.1

Crystal structure of a curved tubulin complex induced by the kinesin-13 Kif2A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.51 Å

Oligo State

hetero-2-2-1-1-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, D.69, E.71, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, I.171, E.183, N.206, Y.224, N.228, I.231 Ligands: MG.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.99, A:A.100, A:N.101, A:S.140, A:G.143, A:G.144, A:T.145, A:G.146, A:V.177, A:E.183, A:N.206, A:N.206, A:Y.224, A:N.228, A:N.228 pi-Stacking: A:Y.224 Salt bridges: B:K.252 GTP.5: 26 residues within 4Å: Chain C: G.10, Q.11, A.12, Q.15, I.16, D.69, D.98, A.99, A.100, N.101, S.140, G.143, G.144, T.145, G.146, P.173, V.177, S.178, T.179, E.183, N.206, Y.224, N.228, I.231 Chain D: K.252 Ligands: MG.6 20 PLIP interactions: 1 interactions with chain D, 19 interactions with chain C Salt bridges: D:K.252 Hydrogen bonds: C:Q.11, C:Q.11, C:Q.11, C:A.12, C:A.99, C:A.100, C:N.101, C:S.140, C:G.143, C:G.144, C:T.145, C:T.145, C:G.146, C:V.177, C:E.183, C:N.206, C:N.206, C:N.228, C:N.228

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: Q.11, E.71 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.71 MG.4: 4 residues within 4Å: Chain B: Q.11, E.69, T.143 Ligands: GDP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.69 MG.6: 4 residues within 4Å: Chain C: D.69, E.71, T.145 Ligands: GTP.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.69, C:D.69 MG.10: 5 residues within 4Å: Chain F: T.187, S.300, D.324, L.325 Ligands: ANP.9 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.187, F:S.300

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

GDP.3: 19 residues within 4Å: Chain B: G.10, Q.11, C.12, A.97, N.99, S.138, G.140, G.141, G.142, T.143, G.144, V.175, D.177, E.181, N.204, Y.222, L.225, N.226 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:T.143, B:T.143, B:G.144, B:D.177, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226 pi-Stacking: B:Y.222 GDP.7: 18 residues within 4Å: Chain D: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, V.175, S.176, E.181, N.204, Y.222, L.225, N.226 Ligands: PO4.8 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:C.12, D:S.138, D:G.141, D:G.142, D:T.143, D:T.143, D:T.143, D:G.144, D:V.175, D:E.181, D:N.204, D:N.204, D:Y.222, D:Y.222, D:N.226 pi-Stacking: D:Y.222, D:Y.222

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 6 residues within 4Å: Chain D: G.10, Q.11, D.67, E.69, T.143 Ligands: GDP.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.11, D:Q.11, D:D.67, D:E.69, D:T.143, D:T.143

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.9: 16 residues within 4Å: Chain F: R.96, P.99, Q.181, T.182, G.183, S.184, G.185, K.186, T.187, H.188, S.299, S.300, L.325, A.326, G.327 Ligands: MG.10 18 PLIP interactions: 18 interactions with chain F Hydrogen bonds: F:R.96, F:G.183, F:S.184, F:G.185, F:K.186, F:K.186, F:K.186, F:K.186, F:T.187, F:T.187, F:H.188, F:H.188, F:S.299, F:S.300, F:S.300, F:S.300, F:G.327 pi-Cation interactions: F:H.188

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trofimova, D. et al., Ternary complex of Kif2A-bound tandem tubulin heterodimers represents a kinesin-13-mediated microtubule depolymerization reaction intermediate. Nat Commun (2018)

Release Date

2018-05-23

Peptides

Tubulin alpha-1B chain: AC
Tubulin beta-2B chain: BD
DARPin: E
Kinesin-like protein KIF2A: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
P

F
E

Tubulin alpha-1B chain

Tubulin beta-2B chain

DARPin

Kinesin-like protein KIF2A

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