4YPD: DAPK1 catalytic domain

Crystal Structure of DAPK1 catalytic domain in complex with the hinge binding fragment 4-methylpyridazine. Determined by X-ray diffraction at 1.4 Å resolution. Released 13 May 2015.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,909
Mol. weight: 34.02 kDa
Ligands: DKG
Released: 13 May 2015

Explore 4YPD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YPD contains 16 α-helices and 16 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
α-helix	9-11	3
β-strand	13-21	9	1
β-strand	25-32	8	1
β-strand	38-45	8	1
β-strand	46	1	2
α-helix	47	1
β-strand	56	1	2
α-helix	58-70	13
β-strand	76	1	3
α-helix	77-78	2
β-strand	79-84	6	1
β-strand	88-94	7	1
β-strand	100	1	3
α-helix	101-108	8
α-helix	113-132	20
β-strand	135-136	2	4
α-helix	142-144	3
β-strand	145-147	3	3
β-strand	157-159	3	3
β-strand	166-167	2	4
β-strand	173	1	5
α-helix	181-183	3
α-helix	186-189	4
β-strand	194	1	5
α-helix	197-212	16
α-helix	222-230	9
α-helix	238-241	4
α-helix	246-253	8
α-helix	260-262	3
α-helix	264-265	2
α-helix	266-271	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Death-associated protein kinase 1	A	protein	294	Homo sapiens	P53355 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4YPD_1 Death-associated protein kinase 1 (chains A)
TVFRQENVDDYYDTGEELGSGQFAVVKKCREKSTGLQYAAKFIKKRRTKSSRRGVSREDI
EREVSILKEIQHPNVITLHEVYENKTDVILILELVAGGELFDFLAEKESLTEEEATEFLK
QILNGVYYLHSLQIAHFDLKPENIMLLDRNVPKPRIKIIDFGLAHKIDFGNEFKNIFGTP
EFVAPEIVNYEPLGLEADMWSIGVITYILLSGASPFLGDTKQETLANVSAVNYEFEDEYF
SNTSALAKDFIRRLLVKDPKKRMTIQDSLQHPWIKPKDTQQALSSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
DKG	4-methylpyridazine	C5 H6 N2	1

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

Crystal Structure of DAPK1 catalytic domain in complex with hinge binding fragments. Grum-Tokars, V.L., Minasov, G., Roy, S.M. et al. To be published.

Other PDB entries of the same protein (UniProt P53355 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6GY5 1.09 Å, Crystal structure of the kelch domain of human KLHL20 in complex with DAPK1 peptide
4PF4 1.13 Å, 1.1A X-ray structure of the apo catalytic domain of death-associated protein kinase 1,…
2W4J 1.3 Å, X-ray structure of a DAP-Kinase 2-277
3GU4 1.35 Å, Crystal structure of DAPKQ23V-AMPPNP
9N2M 1.35 Å, Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-047SRM
5AV4 1.4 Å, Crystal structure of DAPK1-genistein complex in the presence of bromide ions.
7CCW 1.4 Å, Crystal structure of death-associated protein kinase 1 in complex with resveratrol and MES
9N1T 1.43 Å, Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-26-100
3GU6 1.49 Å, Crystal structure of DAPKQ23V-ADP
9N2O 1.49 Å, Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-27-040SRM
9O73 1.49 Å, Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound MW01-30-035SRM
1JKS 1.5 Å, 1.5A X-ray structure of apo form of a catalytic domain of death-associated protein kinase

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