SMTL ID : 8bfm.1

Crystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) in complex with FZ331

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: S.90, P.91, N.92, H.93 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.90, A:N.92, A:N.92, A:H.93 Water bridges: A:S.90, A:Y.95 Salt bridges: A:H.93 SO4.2: 5 residues within 4Å: Chain A: R.74, K.75 Chain B: E.79, R.126, Q.127 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Water bridges: A:K.75, B:E.79, B:R.126, B:D.130 Salt bridges: A:R.74, A:K.75, B:R.126 Hydrogen bonds: B:E.79 SO4.5: 8 residues within 4Å: Chain A: Y.133, H.136, R.137, K.200, C.204, T.269, C.270, E.271 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.270, A:E.271 Water bridges: A:E.271 Salt bridges: A:H.136, A:R.137, A:K.200 SO4.6: 3 residues within 4Å: Chain A: Y.244, Q.296, K.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.244, A:Q.296 Salt bridges: A:K.299 SO4.7: 4 residues within 4Å: Chain A: Y.238, E.239, F.240, R.257 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.239, A:F.240 Water bridges: A:Y.238 Salt bridges: A:R.257 SO4.8: 4 residues within 4Å: Chain B: S.90, P.91, N.92, H.93 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.90, B:N.92, B:N.92, B:H.93 Water bridges: B:Y.95, B:Y.95 Salt bridges: B:H.93 SO4.9: 5 residues within 4Å: Chain A: E.79, R.126, Q.127 Chain B: R.74, K.75 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Salt bridges: B:R.74, B:K.75, A:R.126 Water bridges: A:E.79, A:N.80, A:R.126, A:D.130 SO4.12: 8 residues within 4Å: Chain B: Y.133, H.136, R.137, K.200, C.204, T.269, C.270, E.271 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.270, B:E.271 Salt bridges: B:H.136, B:R.137, B:K.200 SO4.13: 3 residues within 4Å: Chain B: Y.244, Q.296, K.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.296 Salt bridges: B:K.299 SO4.14: 4 residues within 4Å: Chain B: Y.238, E.239, F.240, R.257 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.239, B:E.239, B:F.240 Water bridges: B:Y.238 Salt bridges: B:R.257

4 x QI6: pyrazolo[5,1-a]phthalazin-6-amine(Non-covalent)

QI6.3: 9 residues within 4Å: Chain A: L.29, V.37, A.50, Q.99, L.100, V.101, L.151, S.164, D.165 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.29, A:V.37, A:A.50, A:L.151 Hydrogen bonds: A:V.101 Water bridges: A:L.29 QI6.4: 8 residues within 4Å: Chain A: K.52, I.70, V.82, L.96, M.98, S.164, D.165, F.166 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.70, A:V.82, A:L.96, A:F.166, A:F.166 Hydrogen bonds: A:K.52, A:D.165, A:D.165, A:F.166 QI6.10: 9 residues within 4Å: Chain B: L.29, V.37, A.50, Q.99, L.100, V.101, L.151, S.164, D.165 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.29, B:V.37, B:A.50, B:L.151 Hydrogen bonds: B:V.101 Water bridges: B:L.29 QI6.11: 8 residues within 4Å: Chain B: K.52, I.70, V.82, L.96, M.98, S.164, D.165, F.166 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.70, B:V.82, B:L.96, B:F.166, B:F.166 Hydrogen bonds: B:K.52, B:D.165, B:F.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kraemer, A. et al., Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2). To Be Published

Release Date

2022-11-23

Peptides

Calcium/calmodulin-dependent protein kinase type 1D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Calcium/calmodulin-dependent protein kinase type 1D

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