1NDD: NEDD8

Structure of NEDD8. Determined by X-ray diffraction at 1.6 Å resolution. Released 23 Feb 1999.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,564
Mol. weight: 34.75 kDa
Released: 23 Feb 1999

Explore 1NDD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NDD contains 12 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: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
β-strand	12-16	5	1
β-strand	22	1	2
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	1
β-strand	48-49	2	1
α-helix	50-51	2
β-strand	55	1	2
α-helix	56-59	4
β-strand	66-71	6	1

Chain B: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	102-107	6	3
β-strand	112-116	5	3
β-strand	122	1	4
α-helix	123-134	12
α-helix	138-140	3
β-strand	141-145	5	3
β-strand	148-149	2	3
α-helix	150-151	2
β-strand	155	1	4
β-strand	166-171	6	3

Chain C: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	202-206	5	5
β-strand	212-216	5	5
β-strand	222	1	6
α-helix	223-234	12
α-helix	238-240	3
β-strand	241-245	5	5
β-strand	248-249	2	5
β-strand	255	1	6
α-helix	257-259	3
β-strand	266-271	6	5

Chain D: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	302-306	5	7
β-strand	312-316	5	7
β-strand	322	1	8
α-helix	323-334	12
α-helix	338-340	3
β-strand	341-345	5	7
β-strand	348-349	2	7
β-strand	355	1	8
β-strand	366-371	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein (ubiquitin-like protein NEDD8)	A, B, C, D	protein	76	Homo sapiens	Q15843 (AlphaFold model)

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

>1NDD_1 PROTEIN (UBIQUITIN-LIKE PROTEIN NEDD8) (chains A, B, C, D)
MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYK
ILGGSVLHLVLALRGG

Primary citation

Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. Whitby, F.G., Xia, G., Pickart, C.M. et al. J Biol Chem (1998) 273:34983-34991. DOI 10.1074/jbc.273.52.34983 · PubMed

Other PDB entries of the same protein (UniProt Q15843 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4FBJ 1.6 Å, Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in…
8WZN 1.8 Å, ParkinK211N in complex with phospho NEDD8
2BKR 1.9 Å, NEDD8 NEDP1 complex
4F8C 1.95 Å, Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor…
1XT9 2.2 Å, Crystal Structure of Den1 in complex with Nedd8
8WZO 2.25 Å, Parkin in complex with phospho NEDD8
4HCP 2.52 Å, crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
8CAF 2.66 Å, N8C_Fab3b in complex with NEDD8-CUL1(WHB)
2NVU 2.8 Å, Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like…
3DBH 2.85 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
3DBL 2.9 Å, Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by…
9T7V 2.95 Å, Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub

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