5LF6: Proteasome subunit alpha type-2

Human 20S proteasome complex with Z-LLY-ketoaldehyde at 2.1 Angstrom. Determined by X-ray diffraction at 2.07 Å resolution. Released 17 Aug 2016.

Method: X-ray diffraction
Resolution: 2.07 Å
Organism: Homo sapiens
Chains: 30
Atoms: 51,953
Mol. weight: 724.72 kDa
Ligands: MG, NEN
Released: 17 Aug 2016

Explore 5LF6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5LF6 contains 251 α-helices and 386 β-strands across 30 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: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	20
β-strand	11-16	6	21
β-strand	19-25	7	21
β-strand	28-30	3	20
β-strand	33-36	4	20
β-strand	42-46	5	20
β-strand	49-56	8	20
α-helix	57-77	21
α-helix	85-101	17
β-strand	108-116	9	20
β-strand	119-125	7	20
β-strand	131-133	3	20
β-strand	136-138	3	21
α-helix	142-145	4
α-helix	147-156	10
α-helix	162-179	18
β-strand	180	1	61
β-strand	187-193	7	21
β-strand	196-203	8	21
α-helix	210-213	4

Chain A: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	19-29	11
α-helix	32-33	2
β-strand	34-39	6	1
β-strand	42-48	7	1
β-strand	56	1	2
α-helix	58-60	3
β-strand	65-66	2	3
β-strand	71-77	7	3
α-helix	79-100	22
α-helix	103-105	3
α-helix	106-119	14
β-strand	126	1	4
α-helix	127-129	3
β-strand	131-139	9	3
β-strand	142-148	7	3
β-strand	154-156	3	3
β-strand	157	1	5
β-strand	159-162	4	1
α-helix	166-174	9
α-helix	183-195	13
β-strand	207-213	7	1
β-strand	216-219	4	1
α-helix	220-221	2
α-helix	222-230	9

Chains b and N: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	26
β-strand	11-16	6	26
β-strand	20-22	3	27
β-strand	25-28	4	27
β-strand	34-38	5	28
β-strand	41-47	7	28
α-helix	49-70	22
α-helix	73-75	3
α-helix	76-89	14
α-helix	91-93	3
β-strand	96-104	9	28
β-strand	108-114	7	28
β-strand	121-122	2	28
β-strand	125-128	4	26
α-helix	130-135	6
α-helix	136-142	7
α-helix	149-166	18
β-strand	167	1	58
β-strand	174-180	7	26
β-strand	183-189	7	26
α-helix	191-193	3

Chain B: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	19-30	12
α-helix	32-33	2
β-strand	34-39	6	9
β-strand	42-48	7	9
β-strand	56	1	5
β-strand	65-69	5	10
β-strand	72-78	7	10
α-helix	80-101	22
α-helix	104-106	3
α-helix	107-123	17
β-strand	124	1	11
α-helix	127-130	4
β-strand	132-140	9	10
β-strand	144-150	7	10
β-strand	156-158	3	10
β-strand	159	1	12
β-strand	161-164	4	9
α-helix	168-178	11
α-helix	186-200	15
α-helix	208-210	3
β-strand	211-219	9	9
β-strand	222-227	6	9
α-helix	228-229	2
α-helix	230-245	16

Chains c and d: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	103	1	50

Chain C: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	17-27	11
α-helix	30-31	2
β-strand	32-36	5	16
β-strand	40-46	7	16
β-strand	54	1	12
α-helix	56-59	4
β-strand	62-66	5	17
β-strand	69-75	7	17
α-helix	77-98	22
α-helix	101-103	3
α-helix	104-117	14
β-strand	121	1	18
β-strand	124	1	11
α-helix	125-127	3
β-strand	129-136	8	17
β-strand	142-147	6	17
β-strand	153-155	3	17
β-strand	156	1	19
β-strand	158-161	4	16
α-helix	165-175	11
α-helix	184-198	15
β-strand	206-212	7	16
β-strand	216-219	4	16
α-helix	220-221	2
α-helix	222-233	12

Chains D and R: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14	1
β-strand	15	1	22
α-helix	16	1
β-strand	21	1	22
α-helix	22-31	10
α-helix	35-36	2
β-strand	37-42	6	23
β-strand	45-51	7	23
β-strand	59	1	19
α-helix	61-63	3
β-strand	67-71	5	24
β-strand	74-80	7	24
α-helix	82-103	22
α-helix	106-108	3
α-helix	109-117	9
β-strand	133	1	18
β-strand	139-147	9	24
β-strand	150-156	7	24
β-strand	162-164	3	24
β-strand	165	1	25
β-strand	167-170	4	23
α-helix	174-184	11
α-helix	191-205	15
α-helix	209-210	2
β-strand	215-220	6	23
β-strand	227-228	2	23
α-helix	229-230	2
α-helix	231-238	8

Chain E: 12 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	20-30	11
α-helix	33-34	2
β-strand	35-39	5	29
β-strand	43-49	7	29
α-helix	50-51	2
β-strand	57	1	25
β-strand	63-67	5	30
β-strand	70-76	7	30
α-helix	78-99	22
α-helix	102-104	3
α-helix	105-117	13
α-helix	118-120	3
β-strand	122	1	31
β-strand	130-138	9	30
β-strand	141-147	7	30
β-strand	153-155	3	30
β-strand	156	1	32
β-strand	158-161	4	29
α-helix	165-175	11
α-helix	176-181	6
α-helix	184-196	13
β-strand	210-216	7	29
β-strand	219-225	7	29
α-helix	226-229	4
α-helix	230-233	4

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proteasome subunit alpha type-2	A, O	protein	234	Homo sapiens	P25787 (AlphaFold model)
Proteasome subunit alpha type-4	B, P	protein	261	Homo sapiens	P25789 (AlphaFold model)
Proteasome subunit alpha type-7	C, Q	protein	248	Homo sapiens	O14818 (AlphaFold model)
Proteasome subunit alpha type-5	D, R	protein	241	Homo sapiens	P28066 (AlphaFold model)
Proteasome subunit alpha type-1	E, S	protein	263	Homo sapiens	P25786
Proteasome subunit alpha type-3	F, T	protein	255	Homo sapiens	P25788
Proteasome subunit alpha type-6	G, U	protein	246	Homo sapiens	P60900
Proteasome subunit beta type-7	H, V	protein	234	Homo sapiens	Q99436
Proteasome subunit beta type-3	I, W	protein	205	Homo sapiens	P49720
Proteasome subunit beta type-2	J, X	protein	201	Homo sapiens	P49721
Z-LLY-ketoaldehyde peptide	c, d	protein	4	Homo sapiens
Proteasome subunit beta type-5	K, Y	protein	204	Homo sapiens	P28074

3 more molecules are not listed.

Sequence of entity 1 (A, O), FASTA

>5LF6_1 Proteasome subunit alpha type-2 (chains A, O)
MAERGYSFSLTTFSPSGKLVQIEYALAAVAGGAPSVGIKAANGVVLATEKKQKSILYDER
SVHKVEPITKHIGLVYSGMGPDYRVLVHRARKLAQQYYLVYQEPIPTAQLVQRVASVMQE
YTQSGGVRPFGVSLLICGWNEGRPYLFQSDPSGAYFAWKATAMGKNYVNGKTFLEKRYNE
DLELEDAIHTAILTLKESFEGQMTEDNIEVGICNEAGFRRLTPTEVKDYLAAIA

Sequence of entity 2 (B, P), FASTA

>5LF6_2 Proteasome subunit alpha type-4 (chains B, P)
MSRRYDSRTTIFSPEGRLYQVEYAMEAIGHAGTCLGILANDGVLLAAERRNIHKLLDEVF
FSEKIYKLNEDMACSVAGITSDANVLTNELRLIAQRYLLQYQEPIPCEQLVTALCDIKQA
YTQFGGKRPFGVSLLYIGWDKHYGFQLYQSDPSGNYGGWKATCIGNNSAAAVSMLKQDYK
EGEMTLKSALALAIKVLNKTMDVSKLSAEKVEIATLTRENGKTVIRVLKQKEVEQLIKKH
EEEEAKAEREKKEKEQKEKDK

Sequence of entity 3 (C, Q), FASTA

>5LF6_3 Proteasome subunit alpha type-7 (chains C, Q)
MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGRDIVVLGVEKKSVAKLQDERTVR
KICALDDNVCMAFAGLTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQ
SNGRRPFGISALIVGFDFDGTPRLYQTDPSGTYHAWKANAIGRGAKSVREFLEKNYTDEA
IETDDLTIKLVIKALLEVVQSGGKNIELAVMRRDQSLKILNPEEIEKYVAEIEKEKEENE
KKKQKKAS

Sequence of entity 4 (D, R), FASTA

>5LF6_4 Proteasome subunit alpha type-5 (chains D, R)
MFLTRSEYDRGVNTFSPEGRLFQVEYAIEAIKLGSTAIGIQTSEGVCLAVEKRITSPLME
PSSIEKIVEIDAHIGCAMSGLIADAKTLIDKARVETQNHWFTYNETMTVESVTQAVSNLA
LQFGEEDADPGAMSRPFGVALLFGGVDEKGPQLFHMDPSGTFVQCDARAIGSASEGAQSS
LQEVYHKSMTLKEAIKSSLIILKQVMEEKLNATNIELATVQPGQNFHMFTKEELEEVIKD
I

Sequence of entity 5 (E, S), FASTA

>5LF6_5 Proteasome subunit alpha type-1 (chains E, S)
MFRNQYDNDVTVWSPQGRIHQIEYAMEAVKQGSATVGLKSKTHAVLVALKRAQSELAAHQ
KKILHVDNHIGISIAGLTADARLLCNFMRQECLDSRFVFDRPLPVSRLVSLIGSKTQIPT
QRYGRRPYGVGLLIAGYDDMGPHIFQTCPSANYFDCRAMSIGARSQSARTYLERHMSEFM
ECNLNELVKHGLRALRETLPAEQDLTTKNVSIGIVGKDLEFTIYDDDDVSPFLEGLEERP
QRKAQPAQPADEPAEKADEPMEH

Sequence of entity 6 (F, T), FASTA

>5LF6_6 Proteasome subunit alpha type-3 (chains F, T)
MSSIGTGYDLSASTFSPDGRVFQVEYAMKAVENSSTAIGIRCKDGVVFGVEKLVLSKLYE
EGSNKRLFNVDRHVGMAVAGLLADARSLADIAREEASNFRSNFGYNIPLKHLADRVAMYV
HAYTLYSAVRPFGCSFMLGSYSVNDGAQLYMIDPSGVSYGYWGCAIGKARQAAKTEIEKL
QMKEMTCRDIVKEVAKIIYIVHDEVKDKAFELELSWVGELTNGRHEIVPKDIREEAEKYA
KESLKEEDESDDDNM

Sequence of entity 7 (G, U), FASTA

>5LF6_7 Proteasome subunit alpha type-6 (chains G, U)
MSRGSSAGFDRHITIFSPEGRLYQVEYAFKAINQGGLTSVAVRGKDCAVIVTQKKVPDKL
LDSSTVTHLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIAD
ISQVYTQNAEMRPLGCCMILIGIDEEQGPQVYKCDPAGYYCGFKATAAGVKQTESTSFLE
KKVKKKFDWTFEQTVETAITCLSTVLSIDFKPSEIEVGVVTVENPKFRILTEAEIDAHLV
ALAERD

Sequence of entity 8 (H, V), FASTA

>5LF6_8 Proteasome subunit beta type-7 (chains H, V)
TTIAGVVYKDGIVLGADTRATEGMVVADKNCSKIHFISPNIYCCGAGTAADTDMTTQLIS
SNLELHSLSTGRLPRVVTANRMLKQMLFRYQGYIGAALVLGGVDVTGPHLYSIYPHGSTD
KLPYVTMGSGSLAAMAVFEDKFRPDMEEEEAKNLVSEAIAAGIFNDLGSGSNIDLCVISK
NKLDFLRPYTVPNKKGTRLGRYRCEKGTTAVLTEKITPLEIEVLEETVQTMDTS

Sequence of entity 9 (I, W), FASTA

>5LF6_9 Proteasome subunit beta type-3 (chains I, W)
MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDV
QTVAQRLKFRLNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPF
ICSLDLIGCPMVTDDFVVSGTCAEQMYGMCESLWEPNMDPDHLFETISQAMLNAVDRDAV
SGMGVIVHIIEKDKITTRTLKARMD

Sequence of entity 10 (J, X), FASTA

>5LF6_10 Proteasome subunit beta type-2 (chains J, X)
MEYLIGIQGPDYVLVASDRVAASNIVQMKDDHDKMFKMSEKILLLCVGEAGDTVQFAEYI
QKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSRTPYHVNLLLAGYDEHEGPALYYMDY
LAALAKAPFAAHGYGAFLTLSILDRYYTPTISRERAVELLRKCLEELQKRFILNLPTFSV
RIIDKNGIHDLDNISFPKQGS

Sequence of entity 11 (c, d), FASTA

>5LF6_11 Z-LLY-ketoaldehyde peptide (chains c, d)
XLLX

Sequence of entity 12 (K, Y), FASTA

>5LF6_12 Proteasome subunit beta type-5 (chains K, Y)
TTTLAFKFRHGVIVAADSRATAGAYIASQTVKKVIEINPYLLGTMAGGAADCSFWERLLA
RQCRIYELRNKERISVAAASKLLANMVYQYKGMGLSMGTMICGWDKRGPGLYYVDSEGNR
ISGATFSVGSGSVYAYGVMDRGYSYDLEVEQAYDLARRAIYQATYRDAYSGGAVNLYHVR
EDGWIRVSSDNVADLHEKYSGSTP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	10
NEN	1-ethyl-pyrrolidine-2,5-dione	C6 H9 N O2	8

Water and common crystallization additives (1PE, K, CL) are not listed.

Primary citation

The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design. Schrader, J., Henneberg, F., Mata, R.A. et al. Science (2016) 353:594-598. DOI 10.1126/science.aaf8993 · PubMed

Other PDB entries of the same protein (UniProt P25787 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LE5 1.8 Å, Native human 20S proteasome at 1.8 Angstrom
9TMN 1.85 Å, Human sperm 20S proteasome complex isolated from native source
5LEY 1.9 Å, Human 20S proteasome complex with Oprozomib at 1.9 Angstrom
5LF4 1.99 Å, Human 20S proteasome complex with Delanzomib at 2.0 Angstrom
5LF1 2.0 Å, Human 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom
5LF7 2.0 Å, Human 20S proteasome complex with Ixazomib at 2.0 Angstrom
8UD9 2.04 Å, Structure of human constitutive 20S proteasome complexed with the inhibitor TDI-8304
5LF3 2.1 Å, Human 20S proteasome complex with Bortezomib at 2.1 Angstrom
8BZL 2.14 Å, Human 20S Proteasome in complex with peptide activator peptide BLM42
5LEZ 2.19 Å, Human 20S proteasome complex with Oprozomib in Mg-Acetate at 2.2 Angstrom
5LEX 2.2 Å, Native human 20S proteasome in Mg-Acetate at 2.2 Angstrom
7AWE 2.29 Å, HUMAN IMMUNOPROTEASOME 20S PARTICLE IN COMPLEX WITH [(1R)-2-(1-benzofuran-3-yl)-1-{[(1S,2…

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