SMTL ID : 8qau.1

Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

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

GTP.1: 21 residues within 4Å: Chain A: Q.11, A.12, Q.15, D.98, A.99, A.100, 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 B: L.246, K.252 Ligands: MG.2 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.11, A:D.98, A:A.99, A:A.100, A:N.101, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:E.183, A:N.206, A:N.228, A:N.228 pi-Cation interactions: A:Y.224 Salt bridges: B:K.252, B:K.252, B:K.252, B:K.350

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, E.71, D.98 Ligands: GTP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.98

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

GDP.3: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.141, G.142, T.143, G.144, V.169, D.177, E.181, N.204, Y.222, N.226 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:Q.11, B:C.12, B:S.138, B:G.142, B:T.143, B:G.144, B:D.177, B:E.181, B:E.181, B:N.204, B:N.204, B:N.226, B:N.226 pi-Stacking: B:Y.222, B:Y.222

1 x TA1: TAXOL(Covalent)

TA1.4: 15 residues within 4Å: Chain B: E.22, V.23, D.26, L.215, H.227, L.228, S.234, P.272, T.274, R.276, Q.279, P.358, R.359, G.360, L.361 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.23, B:V.23, B:D.26, B:L.215, B:L.215, B:L.228, B:Q.279, B:P.358, B:L.361 Hydrogen bonds: B:T.274, B:Q.279, B:R.359 Salt bridges: B:R.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Muir, K.W. et al., Mechanism of outer kinetochore assembly on microtubules and its regulation by mitotic error correction. Biorxiv (2023)

Release Date

2024-04-03

Peptides

Tubulin alpha-1A chain: A
Tubulin beta chain: B
Kinetochore protein NDC80: C
Kinetochore protein NUF2: D
DASH complex subunit DAM1: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

E
E

Tubulin alpha-1A chain

Tubulin beta chain

Kinetochore protein NDC80

Kinetochore protein NUF2

DASH complex subunit DAM1

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