5C1B: P97-delta709-728

p97-delta709-728 in complex with a UFD1-SHP peptide. Determined by X-ray diffraction at 3.08 Å resolution. Released 13 Jan 2016.

Method: X-ray diffraction
Resolution: 3.08 Å
Organism: Homo sapiens
Chains: 8
Atoms: 34,659
Mol. weight: 532.94 kDa
Ligands: MG, AGS
Released: 13 Jan 2016

Explore 5C1B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C1B contains 272 α-helices and 196 β-strands across 6 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: 45 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	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	86-91	6
β-strand	99-104	6	1
β-strand	110	1	2
β-strand	113-118	6	3
β-strand	119	1	4
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	2
β-strand	151-155	5	3
β-strand	160-168	9	3
β-strand	173-175	3	2
β-strand	181-183	3	3
α-helix	188	1
β-strand	189	1	4
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
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	279-295	17
β-strand	299-304	6	5
α-helix	306-308	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	5
α-helix	355-358	4
β-strand	365-368	4	5
α-helix	374-383	10
β-strand	389-390	2	6
α-helix	396-402	7
α-helix	408-430	23
α-helix	431-433	3
α-helix	439-443	5
β-strand	446-447	2	6
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	7
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	7
α-helix	524-534	11
β-strand	538-543	6	7
α-helix	544-549	6
α-helix	555-568	14
β-strand	572-577	6	7
α-helix	580-586	7
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	7
α-helix	631-634	4
β-strand	641-644	4	7
α-helix	650-660	11
β-strand	666	1	8
α-helix	672-678	7
α-helix	684-705	22
β-strand	731	1	8
α-helix	733-742	10
α-helix	749-761	13
α-helix	762-766	5

Chain B: 45 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	9
β-strand	38-41	4	9
α-helix	43-48	6
β-strand	56-60	5	9
β-strand	66-73	8	9
β-strand	81-84	4	9
α-helix	86-91	6
β-strand	99-104	6	9
β-strand	110	1	10
β-strand	113-118	6	11
β-strand	119	1	12
α-helix	120-122	3
β-strand	127	1	13
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	144-147	4	10
β-strand	151-155	5	11
β-strand	160-168	9	11
β-strand	173-176	4	10
β-strand	181-183	3	11
α-helix	188	1
β-strand	189	1	12
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-244	5	14
α-helix	251-262	12
β-strand	265-270	6	14
α-helix	271-275	5
α-helix	279-295	17
β-strand	299-304	6	14
α-helix	306-308	3
β-strand	311	1	15
α-helix	313-315	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	14
β-strand	353	1	15
α-helix	355-358	4
β-strand	365-368	4	14
α-helix	374-383	10
β-strand	390	1	16
α-helix	396-402	7
α-helix	408-427	20
β-strand	438	1	13
α-helix	439-444	6
β-strand	447	1	16
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	17
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	17
α-helix	524-534	11
β-strand	538-543	6	17
α-helix	544-549	6
α-helix	555-568	14
β-strand	572-577	6	17
α-helix	580-586	7
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	17
α-helix	631-634	4
β-strand	641-644	4	17
α-helix	650-660	11
β-strand	666	1	18
α-helix	672-678	7
α-helix	684-704	21
β-strand	731	1	18
α-helix	733-742	10
α-helix	749-761	13
α-helix	762-766	5

Chain C: 45 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	19
β-strand	38-41	4	19
α-helix	43-48	6
β-strand	56-60	5	19
β-strand	66-73	8	19
β-strand	81-84	4	19
α-helix	86-91	6
β-strand	99-104	6	19
β-strand	110	1	20
β-strand	113-118	6	21
β-strand	119	1	22
α-helix	120-122	3
β-strand	126-127	2	23
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	20
β-strand	151-155	5	21
β-strand	160-168	9	21
β-strand	173-175	3	20
β-strand	181-183	3	21
α-helix	188	1
β-strand	189	1	22
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-244	5	24
α-helix	251-262	12
β-strand	265-270	6	24
α-helix	271-274	4
α-helix	279-295	17
β-strand	299-304	6	24
α-helix	306-308	3
β-strand	311	1	25
α-helix	313-315	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	24
β-strand	353	1	25
α-helix	355-358	4
β-strand	365-368	4	24
α-helix	374-383	10
β-strand	390	1	26
α-helix	396-402	7
α-helix	408-430	23
β-strand	437-438	2	23
α-helix	439-444	6
β-strand	447	1	26
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	27
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	27
α-helix	524-534	11
β-strand	538-543	6	27
α-helix	544-549	6
α-helix	555-568	14
β-strand	572-577	6	27
α-helix	580-586	7
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	27
α-helix	631-634	4
β-strand	641-644	4	27
α-helix	650-660	11
β-strand	666	1	28
α-helix	672-678	7
α-helix	684-704	21
β-strand	731	1	28
α-helix	733-742	10
α-helix	749-761	13
α-helix	762-766	5

Chain D: 45 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	29
β-strand	38-41	4	29
α-helix	43-48	6
β-strand	56-60	5	29
β-strand	66-73	8	29
β-strand	81-84	4	29
α-helix	86-91	6
β-strand	99-104	6	29
β-strand	110	1	30
β-strand	113-118	6	31
β-strand	119	1	32
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	30
β-strand	151-155	5	31
β-strand	160-168	9	31
β-strand	173-175	3	30
β-strand	181-183	3	31
α-helix	188	1
β-strand	189	1	32
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-244	5	33
α-helix	251-262	12
β-strand	265-270	6	33
α-helix	271-275	5
α-helix	279-295	17
β-strand	299-304	6	33
α-helix	306-308	3
β-strand	311	1	34
α-helix	313-315	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	33
β-strand	353	1	34
α-helix	355-358	4
β-strand	365-368	4	33
α-helix	374-383	10
β-strand	390	1	35
α-helix	396-402	7
α-helix	408-433	26
α-helix	439-444	6
β-strand	447	1	35
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	36
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	36
α-helix	524-534	11
β-strand	538-543	6	36
α-helix	544-547	4
α-helix	555-568	14
β-strand	572-577	6	36
α-helix	580-586	7
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	36
α-helix	631-634	4
β-strand	641-644	4	36
α-helix	650-661	12
β-strand	666	1	37
α-helix	672-678	7
α-helix	684-704	21
β-strand	731	1	37
α-helix	733-741	9
α-helix	749-761	13
α-helix	762-766	5

Chain E: 45 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	38
β-strand	38-41	4	38
α-helix	43-49	7
β-strand	56-60	5	38
β-strand	66-73	8	38
β-strand	81-84	4	38
α-helix	86-92	7
β-strand	99-104	6	38
β-strand	110	1	39
β-strand	113-118	6	40
β-strand	119	1	41
α-helix	120-122	3
β-strand	127	1	42
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	39
β-strand	151-155	5	40
β-strand	160-168	9	40
β-strand	173-175	3	39
β-strand	181-183	3	40
α-helix	188	1
β-strand	189	1	41
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-244	5	43
α-helix	251-262	12
β-strand	265-270	6	43
α-helix	271-275	5
α-helix	279-295	17
β-strand	299-304	6	43
α-helix	306-308	3
β-strand	311	1	44
α-helix	313-315	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	43
β-strand	353	1	44
α-helix	355-358	4
β-strand	365-368	4	43
α-helix	374-383	10
β-strand	389-390	2	45
α-helix	396-402	7
α-helix	408-426	19
β-strand	438	1	42
α-helix	439-444	6
β-strand	446-447	2	45
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	46
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	46
α-helix	524-534	11
β-strand	538-543	6	46
α-helix	544-549	6
α-helix	555-568	14
β-strand	572-577	6	46
α-helix	580-586	7
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	46
α-helix	631-634	4
β-strand	641-644	4	46
α-helix	650-660	11
β-strand	666	1	47
α-helix	672-678	7
α-helix	684-704	21
β-strand	731	1	47
α-helix	733-742	10
α-helix	749-761	13
α-helix	762-766	5

Chain F: 47 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	48
β-strand	38-41	4	48
α-helix	43-48	6
β-strand	56-60	5	48
β-strand	66-73	8	48
β-strand	81-84	4	48
α-helix	86-91	6
β-strand	99-105	7	48
β-strand	110	1	49
β-strand	113-118	6	50
β-strand	119	1	51
α-helix	120-122	3
α-helix	130	1
α-helix	131-135	5
α-helix	136-139	4
β-strand	145-147	3	49
β-strand	151-155	5	50
β-strand	160-168	9	50
β-strand	173-175	3	49
β-strand	181-183	3	50
α-helix	188	1
β-strand	189	1	51
α-helix	190-192	3
α-helix	203-205	3
α-helix	210-225	16
α-helix	227-233	7
α-helix	235-238	4
β-strand	240-244	5	52
α-helix	251-262	12
β-strand	265-270	6	52
α-helix	271-275	5
α-helix	279-295	17
β-strand	299-304	6	52
α-helix	306-308	3
β-strand	311	1	53
α-helix	313-315	3
α-helix	319-333	15
α-helix	334-337	4
β-strand	341-347	7	52
β-strand	353	1	53
α-helix	355-358	4
β-strand	365-368	4	52
α-helix	374-383	10
β-strand	389-390	2	54
α-helix	391	1
α-helix	396-402	7
α-helix	408-425	18
α-helix	427-430	4
α-helix	439-444	6
β-strand	446-447	2	54
α-helix	449-457	9
α-helix	467-468	2
β-strand	470	1	55
α-helix	476-478	3
α-helix	483-489	7
α-helix	490-494	5
α-helix	495-498	4
α-helix	500-506	7
α-helix	509-511	3
β-strand	513-517	5	55
α-helix	524-534	11
β-strand	538-543	6	55
α-helix	544-549	6
α-helix	555-568	14
β-strand	572-577	6	55
α-helix	579-584	6
α-helix	595-610	16
α-helix	613-615	3
β-strand	617-623	7	55
α-helix	631-634	4
β-strand	641-644	4	55
α-helix	650-660	11
β-strand	666	1	56
α-helix	672-678	7
α-helix	684-705	22
β-strand	731	1	56
α-helix	733-742	10
α-helix	749-761	13
α-helix	762-764	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transitional endoplasmic reticulum ATPase	A, B, C, D, E, F	protein	785	Homo sapiens	P55072 (AlphaFold model)
Ubiquitin fusion degradation protein 1 homolog	U, V	protein	21	Homo sapiens	Q92890 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>5C1B_1 Transitional endoplasmic reticulum ATPase (chains A, B, C, D, E, F)
ASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKG
KKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDD
TVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTV
IHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGI
LLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAII
FIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFG
RFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQ
AIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGG
LEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFIS
IKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVI
NQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANL
RKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRPEIRRDHFEEAMR
FARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDND
DDLYG

Sequence of entity 2 (U, V), FASTA

>5C1B_2 Ubiquitin fusion degradation protein 1 homolog (chains U, V)
GELGFRAFSGSGNRLDGKKKG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	12
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	12

Water and common crystallization additives (GOL, CL) are not listed.

Primary citation

Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions. Hanzelmann, P., Schindelin, H. Structure (2016) 24:140-147. DOI 10.1016/j.str.2015.10.027 · 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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