2ZND: Ca2+-free form of des3-20ALG-2

Crystal structure of Ca2+-free form of des3-20ALG-2. Determined by X-ray diffraction at 1.7 Å resolution. Released 9 Sept 2008.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,575
Mol. weight: 21.01 kDa
Ligands: MRD, PO4
Released: 9 Sept 2008

Explore 2ZND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZND contains 8 α-helices and 4 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: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	26-35	10
β-strand	43-44	2	1
α-helix	45-51	7
α-helix	62-72	11
β-strand	79-80	2	1
α-helix	82-102	21
β-strand	109-110	2	2
α-helix	112-121	10
α-helix	128-138	11
β-strand	146-147	2	2
α-helix	148-168	21
α-helix	180-188	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death protein 6	A	protein	172	Homo sapiens	O75340 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2ZND_1 Programmed cell death protein 6 (chains A)
AALPDQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAG
VNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFD
RQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV

Ligands and cofactors

ID	Name	Formula	Copies
MRD	(4R)-2-methylpentane-2,4-diol	C6 H14 O2	5
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Structural Basis for Ca(2+)-Dependent Formation of ALG-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism. Suzuki, H., Kawasaki, M., Inuzuka, T. et al. Structure (2008) 16:1562-1573. DOI 10.1016/j.str.2008.07.012 · PubMed

Other PDB entries of the same protein (UniProt O75340 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ZNE 2.2 Å, Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide
5GQQ 2.2 Å, Structure of ALG-2/HEBP2 Complex
3WXA 2.36 Å, X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide
2ZN9 2.4 Å, Crystal structure of Ca2+-bound form of des3-20ALG-2
3AAJ 2.4 Å, Crystal structure of Ca2+-bound form of des3-23ALG-2deltaGF122
2ZN8 2.7 Å, Crystal structure of Zn2+-bound form of ALG-2
3AAK 2.7 Å, Crystal structure of Zn2+-bound form of des3-20ALG-2F122A
2ZRS 3.1 Å, Crystal structure of Ca2+-bound form of des3-23ALG-2
2ZRT 3.3 Å, Crystal structure of Zn2+-bound form of des3-23ALG-2

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