SMTL ID : 6gyp.1

Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x MET: METHIONINE(Non-covalent)

MET.1: 5 residues within 4Å: Chain A: L.61, F.64, F.538, Q.542 Ligands: PHE.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.61, A:F.64 Hydrogen bonds: A:Q.542

1 x PHE: PHENYLALANINE(Non-covalent)

PHE.2: 5 residues within 4Å: Chain A: S.532, F.533, Y.534 Ligands: MET.1, ASN.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.534

1 x ASN: ASPARAGINE(Non-covalent)

ASN.3: 7 residues within 4Å: Chain A: Y.57, D.60, D.531, S.532 Ligands: PHE.2, ARG.4, THR.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.60

1 x ARG: ARGININE(Non-covalent)

ARG.4: 7 residues within 4Å: Chain A: E.56, Y.57, G.530, D.531 Ligands: ASN.3, THR.5, THR.6 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: T.5, A:D.531 Salt bridges: A:E.56

2 x THR: THREONINE(Non-covalent)

THR.5: 5 residues within 4Å: Chain A: E.56, D.60 Ligands: ASN.3, ARG.4, THR.6 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrogen bonds: R.4, T.5 THR.6: 4 residues within 4Å: Chain A: E.56 Ligands: ARG.4, THR.5, GLN.7 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:E.56, Q.7

1 x GLN: GLUTAMINE(Non-functional Binders)

GLN.7: 1 residues within 4Å: Ligands: THR.6 1 PLIP interactions: 1 Ligand-Ligand interactions Hydrogen bonds: T.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, K. et al., Architecture of the CBF3-centromere complex of the budding yeast kinetochore. Nat. Struct. Mol. Biol. (2018)

Release Date

2018-12-05

Peptides

Centromere DNA-binding protein complex CBF3 subunit B: A
Centromere DNA-binding protein complex CBF3 subunit C: B
Centromere DNA-binding protein complex CBF3 subunit B: C
Suppressor of kinetochore protein 1: D
Centromere DNA-binding protein complex CBF3 subunit A: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

D
D

E
E

Centromere DNA-binding protein complex CBF3 subunit B

Centromere DNA-binding protein complex CBF3 subunit C

Centromere DNA-binding protein complex CBF3 subunit B

Suppressor of kinetochore protein 1

Centromere DNA-binding protein complex CBF3 subunit A

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