4KDL: P97/VCP N

Crystal structure of p97/VCP N in complex with OTU1 UBXL. Determined by X-ray diffraction at 1.81 Å resolution. Released 19 Mar 2014.

Method: X-ray diffraction
Resolution: 1.81 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 2
Atoms: 2,195
Mol. weight: 31.5 kDa
Released: 19 Mar 2014

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

Secondary structure: helices and β-sheets

4KDL contains 15 α-helices and 23 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: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	1
β-strand	38-41	4	1
α-helix	43-48	6
α-helix	51-52	2
β-strand	53	1	2
β-strand	56-60	5	1
β-strand	66-73	8	1
β-strand	81-83	3	1
α-helix	86-91	6
β-strand	99-104	6	1
α-helix	108-109	2
β-strand	110	1	3
α-helix	111	1
β-strand	113-118	6	4
β-strand	119	1	5
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	3
β-strand	151-154	4	4
β-strand	161-169	9	4
β-strand	173-176	4	3
β-strand	181-183	3	4
α-helix	187-188	2
β-strand	189	1	5
α-helix	190	1
α-helix	191-193	3

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	1-7	7	2
β-strand	10-16	7	2
β-strand	21	1	6
α-helix	22-28	7
β-strand	35-38	4	2
β-strand	43-46	4	2
α-helix	54-56	3
β-strand	58	1	6
α-helix	60-62	3
β-strand	68-72	5	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	193	Homo sapiens	P55072 (AlphaFold model)
Ubiquitin thioesterase OTU1	B	protein	90	Saccharomyces cerevisiae	P43558 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4KDL_1 Transitional endoplasmic reticulum ATPase (chains A)
GSHMASMTGGQQMGRGSNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKK
RREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTV
EGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIH
CEGEPIKREDEEE

Sequence of entity 2 (B), FASTA

>4KDL_2 Ubiquitin thioesterase OTU1 (chains B)
GSHMASMTGGQQMGRGSMKLKVTGAGINQVVTLKQDATLNDLIEHINVDVKTMRFGYPPQ
RINLQGEDASLGQTQLDELGINSGEKITIE

Primary citation

Structural Basis for Ovarian Tumor Domain-containing Protein 1 (OTU1) Binding to p97/Valosin-containing Protein (VCP). Kim, S.J., Cho, J., Song, E.J. et al. J Biol Chem (2014) 289:12264-12274. DOI 10.1074/jbc.M113.523936 · PubMed

Other PDB entries of the same protein (UniProt P55072 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5B6C 1.55 Å, Structural Details of Ufd1 binding to p97
7PUX 1.73 Å, Structure of p97 N-D1(L198W) in complex with Fragment TROLL2
3TIW 1.8 Å, Crystal structure of p97N in complex with the C-terminus of gp78
4KDI 1.86 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
5EPP 1.88 Å, Structural Insights into the Interaction of p97 N-terminus Domain and VBM Motif in…
3EBB 1.9 Å, PLAP/P97 complex
6G2V 1.9 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
6G2Z 1.92 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation
4KO8 1.98 Å, Structure of p97 N-D1 R155H mutant in complex with ATPgS
3QQ8 2.0 Å, Crystal structure of p97-N in complex with FAF1-UBX
3QWZ 2.0 Å, Crystal structure of FAF1 UBX-p97N-domain complex
6G2X 2.08 Å, Crystal structure of the p97 D2 domain in a helical split-washer conformation

Browse structure collections

About this viewer

MolViewer shows 4KDL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.