SMTL ID : 6ya7.1

Cdc7-Dbf4 bound to an Mcm2-S40 derived bivalent substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.197, C.199, C.206, C.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.197, A:C.199, A:C.206, A:C.209 ZN.2: 4 residues within 4Å: Chain A: N.146, D.160 Chain C: A.8 Ligands: ADP.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.160, H2O.1 ZN.3: 3 residues within 4Å: Chain A: C.295, K.297 Chain B: M.33 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.295 ZN.5: 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

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

ADP.4: 20 residues within 4Å: Chain A: I.28, G.29, E.30, G.31, S.34, V.36, A.52, K.54, M.82, M.98, P.99, Y.100, L.101, H.103, S.145, N.146, L.148, D.160 Chain C: A.8 Ligands: ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.34, A:S.34, A:P.99, A:L.101 Water bridges: A:T.32, A:F.33, A:S.34, A:K.54, A:H.103, A:S.145, A:S.145, A:N.146 Salt bridges: A:K.54, A:K.54

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
DNA replication licensing factor MCM2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

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

DNA replication licensing factor MCM2

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