8BDU: PIH1 domain-containing protein 1

H33 variant of DoBi scaffold based on PIH1D1 N-terminal domain. Determined by X-ray diffraction at 2.47 Å resolution. Released 16 Aug 2023.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,071
Mol. weight: 34.15 kDa
Released: 16 Aug 2023

Explore 8BDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8BDU contains 10 α-helices and 15 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: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	1
β-strand	23-31	9	2
β-strand	36-44	9	2
α-helix	48-49	2
α-helix	55-64	10
β-strand	71-73	3	1
α-helix	76-78	3
β-strand	79-82	4	2
β-strand	88-97	10	2
α-helix	98-105	8
α-helix	108-125	18
β-strand	135-136	2	2

Chain B: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	3
β-strand	23-32	10	3
β-strand	35-44	10	3
α-helix	48-49	2
α-helix	55-63	9
β-strand	71-73	3	3
α-helix	76-78	3
β-strand	79-82	4	3
β-strand	88-97	10	3
α-helix	98-105	8
α-helix	108-126	19
β-strand	130	1	3
β-strand	135-137	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PIH1 domain-containing protein 1	A, B	protein	152	Homo sapiens	Q9NWS0 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8BDU_1 PIH1 domain-containing protein 1 (chains A, B)
MAWSHPQFEKSAALEVLFQGPGQPGFCIKTNSSEGKVFINICHSPSIPPPADVTEEELLQ
MLEEDQAGFRIPMSLGEPHAELDAKGQGCTAYDVAVNSDFYRRMQNSDFLRYLVISIAAS
GLESKYRLSLSPIWWMMKNRPFMGSISQQNIR

Primary citation

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10. Kolenko, P., Mikulecky, P., Pham, P.N. et al. J Appl Crystallogr (2023) 56:1261-1266. DOI 10.1107/S160057672300479X · PubMed

Other PDB entries of the same protein (UniProt Q9NWS0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AVC 1.2 Å, DoBi scaffold based on PIH1D1 N-terminal domain
9THX 1.36 Å, G14 variant of 57aBi scaffold crystallized in I212121
4PSF 1.58 Å, PIH1D1 N-terminal domain
9TIA 2.07 Å, G14 variant of 57aBi scaffold crystallized in P6422
9TJQ 2.19 Å, G14 variant of 57aBi scaffold crystallized in P6422
4PSI 2.45 Å, PIH1D1/phospho-Tel2 complex
6GXZ 2.96 Å, Crystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex

Browse structure collections

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