2BKQ: NEDD8 protease

NEDD8 protease. Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Feb 2005.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 7,017
Mol. weight: 96.29 kDa
Released: 21 Feb 2005

Explore 2BKQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2BKQ contains 62 α-helices and 28 β-strands across 4 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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	1
β-strand	11-14	4	1
α-helix	15-18	4
α-helix	19-21	3
α-helix	25-27	3
α-helix	29-38	10
α-helix	39-43	5
α-helix	45-47	3
β-strand	51-54	4	2
α-helix	56-63	8
α-helix	68-73	6
α-helix	76-78	3
α-helix	80-82	3
β-strand	85-92	8	2
β-strand	102-109	8	2
β-strand	114-118	5	2
α-helix	126-140	15
β-strand	149-151	3	2
α-helix	155-157	3
α-helix	160-162	3
α-helix	163-179	17
α-helix	186-189	4
α-helix	192-210	19

Chain B: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	3
β-strand	11-14	4	3
α-helix	15-18	4
α-helix	19-21	3
α-helix	25-27	3
α-helix	29-38	10
α-helix	39-43	5
α-helix	45-47	3
β-strand	51-54	4	4
α-helix	56-64	9
α-helix	68-75	8
α-helix	76-78	3
α-helix	80-82	3
β-strand	85-91	7	4
α-helix	96-98	3
β-strand	103-109	7	4
β-strand	114-118	5	4
α-helix	126-140	15
β-strand	149-151	3	4
α-helix	160-162	3
α-helix	163-179	17
α-helix	186-189	4
α-helix	192-209	18

Chain C: 14 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	5
β-strand	11-14	4	5
α-helix	15-19	5
α-helix	25-27	3
α-helix	29-38	10
α-helix	39-43	5
α-helix	45-47	3
β-strand	51-54	4	6
α-helix	56-64	9
α-helix	68-75	8
α-helix	76-78	3
α-helix	80-82	3
β-strand	85-91	7	6
α-helix	96-98	3
β-strand	103-109	7	6
β-strand	114-119	6	6
α-helix	126-140	15
β-strand	149-151	3	6
α-helix	163-179	17
α-helix	186-189	4
α-helix	192-209	18

Chain D: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	7
β-strand	11-14	4	7
α-helix	15-19	5
α-helix	25-27	3
α-helix	29-38	10
α-helix	39-43	5
α-helix	45-47	3
β-strand	51-54	4	8
α-helix	56-63	8
α-helix	68-75	8
α-helix	76-78	3
α-helix	80-82	3
β-strand	85-92	8	8
β-strand	102-109	8	8
α-helix	110-112	3
β-strand	114-118	5	8
α-helix	126-139	14
β-strand	149-151	3	8
α-helix	152-153	2
α-helix	160-162	3
α-helix	163-179	17
α-helix	186-189	4
α-helix	192-210	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sentrin-specific protease 8	A, B, C, D	protein	212	HOMO SAPIENS	Q96LD8 (AlphaFold model)

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

>2BKQ_1 SENTRIN-SPECIFIC PROTEASE 8 (chains A, B, C, D)
MDPVVLSYMDSLLRQSDVSLLDPPSWLNDHIIGFAFEYFANSQFHDSSDHVSFISPEVTQ
FIKCTSNPAEIAMFLEPLDLPNKRVVFLAINDNSNQAAGGSHWSLLVYLQDKNSFFHYDS
HSRSNSVHAKQVAEKLEAFLGRKGDKLAFVEEKAPAQQNSYDCGMYVICNTEALCQNFFR
QQTESLLQLLTPAYITKKRGEWKDLIATLAKK

Primary citation

Structural Basis of Nedd8 Ubiquitin Discrimination by the Deneddylating Enzyme Nedp1. Shen, L.N., Liu, H., Dong, C. et al. EMBO J (2005) 24:1341. DOI 10.1038/SJ.EMBOJ.7600628 · PubMed

Other PDB entries of the same protein (UniProt Q96LD8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2BKR 1.9 Å, NEDD8 NEDP1 complex
1XT9 2.2 Å, Crystal Structure of Den1 in complex with Nedd8

Browse structure collections

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