SMTL ID : 6ya8.1

Cdc7-Dbf4 bound to ADP-BeF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 19 residues within 4Å: Chain A: I.29, G.32, S.35, V.37, A.53, K.55, M.83, M.99, P.100, Y.101, L.102, H.104, S.146, N.147, L.149, D.161 Ligands: MG.2, BEF.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.35, A:P.100, A:L.102, A:D.161 Water bridges: A:G.32, A:S.35, A:S.35, A:H.104, A:S.146, A:S.146, A:N.147, A:D.161, A:G.163 Salt bridges: A:K.55, A:K.55

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: N.147, D.161 Ligands: ADP.1, BEF.3, MG.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.161, H2O.5 MG.4: 4 residues within 4Å: Chain A: D.161 Ligands: ADP.1, MG.2, BEF.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.161, A:D.161, H2O.5, H2O.7

1 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.3: 7 residues within 4Å: Chain A: D.142, K.144, N.147, D.161 Ligands: ADP.1, MG.2, MG.4 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.198, C.200, C.207, C.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.198, A:C.200, A:C.207, A:C.210 ZN.6: 4 residues within 4Å: Chain B: C.90, C.93, H.103, H.109 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.90, B:C.93, B:H.103, B:H.109

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dick, S.D. et al., Structural Basis for the Activation and Target Site Specificity of CDC7 Kinase. Structure (2020)

Release Date

2020-05-27

Peptides

Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase: A
Protein DBF4 homolog A: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase,Cell division cycle 7-related protein kinase

Protein DBF4 homolog A

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