SMTL ID : 8r9s.1 (1 other biounit)

A soakable crystal form of human CDK7 in complex with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.78 Å

Oligo State

monomer

Ligands

2 x PE3: 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL(Non-functional Binders)

PE3.1: 5 residues within 4Å: Chain A: R.86, K.89, K.185, S.186, F.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.89, A:K.89, A:K.185, A:S.186 PE3.3: 1 residues within 4Å: Chain A: H.72 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.72

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: K.185, F.187, R.213, M.214, Y.215 No protein-ligand interaction detected (PLIP)

1 x YPK: [(3S)-1-[4-(dimethylamino)butanoyl]pyrrolidin-3-yl] 4-[(5-methyl-3-propan-2-yl-pyrazolo[1,5-a]pyrimidin-7-yl)amino]piperidine-1-carboxylate(Covalent)

YPK.4: 17 residues within 4Å: Chain A: L.43, V.51, A.64, I.100, F.116, D.117, F.118, M.119, E.120, T.121, D.122, V.125, L.169, A.179, P.335, N.336, C.337 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.43, A:I.100, A:F.116, A:F.116, A:F.118, A:T.121, A:L.169 Hydrogen bonds: A:M.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mukherjee, M. et al., Protein engineering enables a soakable crystal form of human CDK7 primed for high-throughput crystallography and structure-based drug design. Structure (2024)

Release Date

2024-05-29

Peptides

Cyclin-dependent kinase 7: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cyclin-dependent kinase 7

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