5DYG: P97 N-D1 L198W mutant

Structure of p97 N-D1 L198W mutant in complex with ADP. Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Feb 2016.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,642
Mol. weight: 52.82 kDa
Ligands: ADP
Released: 10 Feb 2016

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

Secondary structure: helices and β-sheets

5DYG contains 27 α-helices and 24 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: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	1
β-strand	38-41	4	1
α-helix	43-49	7
β-strand	56-60	5	1
β-strand	66-73	8	1
β-strand	81-84	4	1
α-helix	86-92	7
β-strand	99-104	6	1
β-strand	110	1	2
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-123	4
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	2
β-strand	151-156	6	3
β-strand	159-169	11	3
β-strand	173-176	4	2
β-strand	181-183	3	3
α-helix	187-188	2
β-strand	189	1	4
α-helix	190	1
α-helix	191-193	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	229-232	4
α-helix	235-238	4
β-strand	240-244	5	5
α-helix	251-262	12
β-strand	265-270	6	5
α-helix	271-275	5
α-helix	278	1
α-helix	281-295	15
β-strand	299-304	6	5
α-helix	306-308	3
β-strand	311	1	6
α-helix	319-333	15
α-helix	335-337	3
β-strand	341-347	7	5
β-strand	353	1	6
α-helix	355-358	4
β-strand	365-368	4	5
α-helix	374-385	12
β-strand	389-390	2	7
α-helix	396-402	7
α-helix	408-432	25
α-helix	435-437	3
α-helix	439-444	6
β-strand	446-447	2	7
α-helix	449-456	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A	protein	468	Homo sapiens	P55072 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5DYG_1 Transitional endoplasmic reticulum ATPase (chains A)
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLK
GKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDT
VIHCEGEPIKREDEEESWNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAI
IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF
GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNRSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

Primary citation

Role of the D1-D2 Linker of Human VCP/p97 in the Asymmetry and ATPase Activity of the D1-domain. Tang, W.K., Xia, D. Sci Rep (2016) 6:20037-20037. DOI 10.1038/srep20037 · 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
4KDL 1.81 Å, Crystal structure of p97/VCP N in complex with OTU1 UBXL
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

Browse structure collections

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