MolNFT v1 · #15719 · protein

Structure of NEDD8

1NDD · Protein (ubiquitin-like protein NEDD8): “Structure of NEDD8”. X-ray diffraction, 2 ligands (SO4, CL), 2 pockets (best druggability 0.32). MolNFT v1 #15719 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NDD
Type: protein
Length: 296 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (ubiquitin-like protein NEDD8)
UniProt: Q15843
Ligands: SO4, CL
Pockets: 2 · best druggability 0.32

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (ubiquitin-like protein NEDD8)	protein	74	26% helix, 34% strand	Q15843
B	Protein (ubiquitin-like protein NEDD8)	protein	76	20% helix, 34% strand	Q15843
C, D	Protein (ubiquitin-like protein NEDD8)	protein	73	25% helix, 34% strand	Q15843

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A, C, D
CL · Chloride ion · ion · 2 copies · chains A, D, B, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.32	0.75	22	empty
2	66	0.30	0.74	18	SO4

Interfaces

6 interfaces between chains.

A–D · 825 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 805 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 391 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 301 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 285 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1NDD · Structure of NEDD8 · the same entry in another collection · chain B against B, TM-score 1.00
Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q15843
Elsewhere: RCSB PDB 1NDD · PDBe 1NDD · UniProt Q15843

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