4KO8: P97 N-D1 R155H mutant

Structure of p97 N-D1 R155H mutant in complex with ATPgS. Determined by X-ray diffraction at 1.98 Å resolution. Released 13 Nov 2013.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,392
Mol. weight: 110.22 kDa
Ligands: MG, AGS
Released: 13 Nov 2013

Explore 4KO8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4KO8 contains 64 α-helices and 48 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: 32 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	25-30	6	1
β-strand	38-41	4	1
α-helix	43-48	6
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
α-helix	108-109	2
β-strand	110	1	2
α-helix	111	1
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-122	3
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
α-helix	180	1
β-strand	181-183	3	3
α-helix	188	1
β-strand	189	1	4
α-helix	190	1
α-helix	191-198	8
α-helix	203-205	3
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	5
α-helix	251-261	11
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
β-strand	341-347	7	5
α-helix	350-352	3
β-strand	353	1	6
α-helix	355-358	4
β-strand	365-368	4	5
α-helix	374-385	12
β-strand	390	1	7
α-helix	396-401	6
α-helix	408-424	17
α-helix	439-444	6
β-strand	447	1	7
α-helix	449-457	9

Chain B: 32 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	19-21	3
β-strand	25-30	6	8
β-strand	38-41	4	8
α-helix	43-48	6
β-strand	56-60	5	8
β-strand	66-73	8	8
β-strand	81-84	4	8
α-helix	86-92	7
β-strand	99-104	6	8
α-helix	108-109	2
β-strand	110	1	9
α-helix	111	1
β-strand	113-118	6	10
β-strand	119	1	11
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	9
β-strand	151-156	6	10
β-strand	159-169	11	10
β-strand	173-176	4	9
α-helix	180	1
β-strand	181-183	3	10
α-helix	188	1
β-strand	189	1	11
α-helix	190	1
α-helix	191-198	8
α-helix	203-205	3
α-helix	210-216	7
α-helix	217-221	5
α-helix	222-225	4
α-helix	227-233	7
α-helix	236-238	3
β-strand	240-244	5	12
α-helix	251-261	11
β-strand	265-270	6	12
α-helix	271-275	5
α-helix	278	1
α-helix	281-295	15
β-strand	299-304	6	12
α-helix	306-308	3
β-strand	311	1	13
α-helix	319-334	16
β-strand	341-347	7	12
α-helix	350-352	3
β-strand	353	1	13
α-helix	355-358	4
β-strand	365-368	4	12
α-helix	374-385	12
β-strand	390	1	14
α-helix	396-401	6
α-helix	408-424	17
α-helix	439-444	6
β-strand	447	1	14
α-helix	449-457	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A, B	protein	489	Homo sapiens	P55072 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4KO8_1 Transitional endoplasmic reticulum ATPase (chains A, B)
MASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLK
GKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPID
DTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVETDPSPYCIVAPDT
VIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRG
ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAI
IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF
GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL
QAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIG
GRSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	2

Primary citation

Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants. Tang, W.K., Xia, D. J Biol Chem (2013) 288:36624-36635. DOI 10.1074/jbc.M113.488924 · 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
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

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