MolNFT v1 · #165393 · protein

Ubiquitin ligation to substrate by a cullin-ring E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric B-TRCP1DD-ikba- UB~UBE2D2

6TTU · F-BOX/WD repeat-containing protein 1A: “Ubiquitin ligation to substrate by a cullin-ring E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1…”. Electron microscopy, 1 ligand (ZN), 18 pockets (best druggability 0.79). MolNFT v1 #165393 on…

PDB: 6TTU
Type: protein
Length: 1,604 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: F-BOX/WD repeat-containing protein 1A; S-phase kinase-associated protein 1; Cullin-1…
EC: 2.3.2.27, 2.3.2.32, 2.3.2.23, 2.3.2.24
UniProt: Q9Y297, P63208, Q13616, Q15843, P62877, P62837, P0CG48
Ligands: ZN
Pockets: 18 · best druggability 0.79

Structure

electron microscopy · 8 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
T	F-BOX/WD repeat-containing protein 1A	protein	394	23% helix, 40% strand	Q9Y297
S	S-phase kinase-associated protein 1	protein	123	59% helix, 10% strand	P63208
C	Cullin-1	protein	701	63% helix, 4% strand	Q13616
N	NEDD8	protein	77	12% helix, 35% strand	Q15843
R	E3 ubiquitin-protein ligase RBX1 (EC 2.3.2.27, 2.3.2.32)	protein	79	18% helix, 24% strand	P62877
D	Ubiquitin-conjugating enzyme E2 D2 (EC 2.3.2.23, 2.3.2.24)	protein	146	38% helix, 18% strand	P62837
U	Polyubiquitin-C	protein	75	25% helix, 28% strand	P0CG48
I	Cys-lys-lys-ala-arg-his-asp-sep-gly	protein	9	0% helix, 0% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains R

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

Pockets

18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	110	0.79	0.97	27	empty
2	881	0.77	0.80	104	empty
3	77	0.73	0.96	18	empty
4	554	0.71	0.80	48	empty
5	529	0.68	0.78	48	empty

Interfaces

16 interfaces between chains.

C–R · 1600 Å² buried · 24 hydrogen bonds · protein-protein
C–N · 1124 Å² buried · 15 hydrogen bonds · protein-protein
T–S · 1047 Å² buried · 2 hydrogen bonds · protein-protein
D–U · 872 Å² buried · 8 hydrogen bonds · protein-protein
N–D · 686 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide, 1 isopeptide, 1 modified (disulfide, isopeptide, phosphorylation).

Compared structures

6TTU · Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution… · the same entry in another collection · chain I against I, TM-score 1.00
Q9Y297 · AlphaFold monomer V2.0 prediction for F-BOX/WD repeat-containing protein 1A (Q9Y297) · a predicted model of the same protein · chain T against A, TM-score 0.97
P63208 · AlphaFold monomer V2.0 prediction for S-phase kinase-associated protein 1 (P63208) · a predicted model of the same protein · chain S against A, TM-score 0.92
Q15843 · AlphaFold monomer V2.0 prediction for NEDD8 (Q15843) · a predicted model of the same protein · chain N against A, TM-score 0.92
Q13616 · AlphaFold monomer V2.0 prediction for cullin-1 (Q13616) · a predicted model of the same protein · chain C against A, TM-score 0.86

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 Q9Y297
Every structure of UniProt P63208
Every structure of UniProt Q13616
Every structure of UniProt Q15843
Every structure of UniProt P62877
Every structure of UniProt P62837
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 6TTU · PDBe 6TTU · UniProt Q9Y297 · UniProt P63208 · UniProt Q13616 · UniProt Q15843 · UniProt P62877 · UniProt P62837 · UniProt P0CG48

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