SMTL ID : 3iz0.1

Human Ndc80 Bonsai Decorated Microtubule

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-2-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: Y.282, H.283 No protein-ligand interaction detected (PLIP)

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Q.11, D.69, E.71 Ligands: GTP.3 No protein-ligand interaction detected (PLIP)

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

GTP.3: 22 residues within 4Å: Chain A: G.10, Q.11, A.12, Q.15, 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, L.227, N.228 Chain B: L.246, K.252 Ligands: MG.2 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.11, A:Q.11, A:A.12, A:A.100, A:A.100, A:N.101, A:S.140, A:G.144, A:T.145, A:G.146, A:T.179, A:T.179, A:E.183, A:N.206, A:Y.224, A:N.228, A:N.228, A:N.228 pi-Stacking: A:Y.224, A:Y.224 Salt bridges: B:K.252, B:K.252

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

GDP.4: 15 residues within 4Å: Chain B: G.10, Q.11, C.12, Q.15, S.138, G.140, G.141, G.142, T.143, G.144, D.177, E.181, N.204, Y.222, N.226 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:T.143, B:D.177, B:E.181, B:N.204, B:Y.222, B:N.226, B:N.226, B:N.226

1 x TA1: TAXOL(Non-covalent)

TA1.5: 19 residues within 4Å: Chain B: E.22, V.23, D.26, E.27, L.215, D.224, H.227, L.228, A.231, S.234, F.270, P.272, L.273, T.274, S.275, R.276, P.358, R.359, G.360 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.23, B:D.26, B:L.215, B:H.227, B:L.228, B:F.270, B:F.270, B:F.270, B:P.358 Hydrogen bonds: B:T.274, B:P.358, B:G.360 pi-Stacking: B:H.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alushin, G.M. et al., The Ndc80 kinetochore complex forms oligomeric arrays along microtubules. Nature (2010)

Release Date

2010-10-13

Peptides

alpha tubulin, Chain A from PDB 1JFF: A
beta tubulin, Chain B from PDB 1JFF: B
NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai): CE
NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai): DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E
E

D
D

F
F

alpha tubulin, Chain A from PDB 1JFF

beta tubulin, Chain B from PDB 1JFF

NDC80-SPC25 chimera protein, Chain B from PDB 2VE7 (Ndc80 bonsai)

NUF2-SPC24 chimera protein, Chain D from PDB 2VE7 (Ndc80 bonsai)

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