5Z7A: NDP52 SKICH region

Crystal structure of NDP52 SKICH region. Determined by X-ray diffraction at 2.38 Å resolution. Released 2 Jan 2019.

Method: X-ray diffraction
Resolution: 2.38 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,889
Mol. weight: 30.55 kDa
Ligands: DTT
Released: 2 Jan 2019

Explore 5Z7A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z7A contains 7 α-helices and 19 β-strands across 2 chains. 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: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	1
β-strand	31	1	2
β-strand	38-44	7	1
β-strand	55-60	6	3
α-helix	66-68	3
β-strand	69-74	6	3
β-strand	89-93	5	1
α-helix	94	1
α-helix	95-97	3
β-strand	105-110	6	3
β-strand	116-119	4	3
α-helix	120-122	3
β-strand	123	1	3
β-strand	124	1	2

Chain B: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	4
β-strand	31	1	5
β-strand	38-44	7	4
β-strand	55-60	6	5
α-helix	66-68	3
β-strand	71-74	4	5
α-helix	75-76	2
β-strand	90-93	4	4
β-strand	104-110	7	5
β-strand	116-119	4	5
α-helix	120-122	3
β-strand	123-124	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Calcium-binding and coiled-coil domain-containing protein 2	A, B	protein	126	Homo sapiens	Q13137 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5Z7A_1 Calcium-binding and coiled-coil domain-containing protein 2 (chains A, B)
MEETIKDPPTSAVLLDHCHFSQVIFNSVEKFYIPGGDVTCHYTFTQHFIPRRKDWIGIFR
VGWKTTREYYTFMWVTLPIDLNNKSAKQQEVQFKAYYLPKDDEYYQFCYVDEDGVVRGAS
IPFQFR

Ligands and cofactors

ID	Name	Formula	Copies
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1

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

Primary citation

Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1. Fu, T., Liu, J., Wang, Y. et al. Proc Natl Acad Sci U S A (2018) 115:E11651-E11660. DOI 10.1073/pnas.1811421115 · PubMed

Other PDB entries of the same protein (UniProt Q13137 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3VVV 1.35 Å, Skich domain of NDP52
5Z7L 2.02 Å, Crystal structure of NDP52 SKICH region in complex with NAP1
4GXL 2.02 Å, The crystal structure of Galectin-8 C-CRD in complex with NDP52
4XKL 2.1 Å, Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin
3VVW 2.5 Å, NDP52 in complex with LC3C
4HAN 2.55 Å, Crystal structure of Galectin 8 with NDP52 peptide
7EAA 2.6 Å, crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain
2MXP Solution structure of NDP52 ubiquitin-binding zinc finger
5AAQ TBK1 recruitment to cytosol-invading Salmonella induces anti- bacterial autophagy

Browse structure collections

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