5DIN: Ligand of Numb protein X 2

Structural Basis for the Indispensable Role of a Unique Zinc Finger Motif in LNX2 Ubiquitination. Determined by X-ray diffraction at 1.86 Å resolution. Released 14 Oct 2015.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,260
Mol. weight: 31.4 kDa
Ligands: ZN
Released: 14 Oct 2015

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

Secondary structure: helices and β-sheets

5DIN contains 17 α-helices and 20 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: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	1
α-helix	24-26	3
α-helix	27-29	3
β-strand	30	1	2
β-strand	37	1	2
β-strand	41-43	3	3
β-strand	49-51	3	3
α-helix	52-58	7
β-strand	64	1	4
β-strand	71	1	4
α-helix	74-76	3
β-strand	78-79	2	3
α-helix	80-81	2
α-helix	82-89	8
β-strand	92-94	3	1
β-strand	104-106	3	1
α-helix	107-109	3
α-helix	110-116	7

Chain B: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	20-21	2	5
α-helix	24-26	3
α-helix	27-29	3
β-strand	30	1	6
β-strand	37	1	6
β-strand	41-43	3	7
β-strand	49-51	3	7
α-helix	52-58	7
β-strand	64	1	8
β-strand	71	1	8
α-helix	74-76	3
β-strand	78-79	2	7
α-helix	80-81	2
α-helix	82-89	8
β-strand	92-94	3	5
β-strand	104-106	3	5
α-helix	107-109	3
α-helix	110-116	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ligand of Numb protein X 2	A, B	protein	130	Homo sapiens	Q8N448 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DIN_1 Ligand of Numb protein X 2 (chains A, B)
EFNPLCFECGQQHWTRENHLYNYQNEVDDDLVCHICLQPLLQPLDTPCGHTFCYKCLRNF
LQEKDFCPLDRKRLHFKLCKKSSILVHKLLDKLLVLCPFSSVCKDVMQRCDLEAHLKNRC
PGASHRRVAL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

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

Primary citation

Structural basis for the indispensable role of a unique zinc finger motif in LNX2 ubiquitination. Nayak, D., Sivaraman, J. Oncotarget (2015) 6:34342-34357. DOI 10.18632/oncotarget.5326 · PubMed

Other PDB entries of the same protein (UniProt Q8N448 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5E1Y 1.01 Å, PDZ2 of LNX2 at 277K, model with alternate conformations
5E21 1.01 Å, PDZ2 of LNX2 at 277K,single conformer model
2VWR 1.3 Å, Crystal structure of the second pdz domain of numb-binding protein 2
5E22 1.8 Å, The second PDZ domain of Ligand of Numb protein X 2 in the presence of an electric field…
5E11 1.8 Å, Second PDZ domain of Ligand of Numb protein X 2 by Laue crystallography (no electric…
7QCT 3.2 Å, PDZ2 of LNX2 with SARS-CoV-2_E PBM complex

Browse structure collections

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