SMTL ID : 9qcv.1

Cryo-EM structure of CAK-CDK2-cyclin A2 bound to AMP-PNP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.50 Å

Oligo State

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

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: I.13, G.16, T.17, V.21, A.34, K.36, F.83, E.84, F.85, L.86, L.137, D.148 Chain E: Q.67, H.92, R.93 Ligands: MG.2 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:T.17, A:T.17, A:T.17, A:E.84, A:L.86, A:D.148, A:D.148, E:Q.67, E:Q.67, E:H.92, E:R.93, E:R.93 Salt bridges: A:K.36 ANP.3: 14 residues within 4Å: Chain E: L.63, G.64, G.66, Q.67, V.71, A.84, I.120, D.137, F.138, M.139, K.184, L.189, D.200 Ligands: MG.4 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.67, E:D.137, E:M.139, E:K.184, E:K.184

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.148 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.148, A:D.148 MG.4: 3 residues within 4Å: Chain E: N.187, D.200 Ligands: ANP.3 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cushing, V.I. et al., Structural basis of T-loop-independent recognition and activation of CDKs by the CDK-activating kinase. To Be Published

Release Date

2025-10-15

Peptides

Cyclin-dependent kinase 2: A
Cyclin-A2: B
CDK-activating kinase assembly factor MAT1: C
Cyclin-H: D
Cyclin-dependent kinase 7: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
L

C
H

D
I

E
J

Cyclin-dependent kinase 2

Cyclin-A2

CDK-activating kinase assembly factor MAT1

Cyclin-H

Cyclin-dependent kinase 7

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