MolNFT v1 · #20111 · protein

APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex

1R4M · Amyloid beta precursor protein-binding protein 1: “APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #20111 on GenesisL1: 3D structure, binding…

PDB: 1R4M
Type: protein
Length: 4,040 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Amyloid beta precursor protein-binding protein 1; Ubiquitin-activating enzyme E1C…
UniProt: Q13564, Q8TBC4, Q15843
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Amyloid beta precursor protein-binding protein 1	protein	516	53% helix, 10% strand	Q13564
B, D, F, H	Ubiquitin-activating enzyme E1C	protein	418	37% helix, 13% strand	Q8TBC4
I, J, K, L	Ubiquitin-like protein NEDD8	protein	76	24% helix, 26% strand	Q15843

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains D, J, F, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1092	0.81	0.83	98	empty
2	1190	0.80	0.81	110	empty
3	538	0.77	0.84	59	empty
4	548	0.76	0.83	60	empty
5	561	0.76	0.83	61	empty

Interfaces

20 interfaces between chains.

E–F · 3631 Å² buried · 59 hydrogen bonds · protein-protein
G–H · 3631 Å² buried · 57 hydrogen bonds · protein-protein
C–D · 3612 Å² buried · 54 hydrogen bonds · protein-protein
A–B · 3597 Å² buried · 54 hydrogen bonds · protein-protein
B–I · 1274 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

1R4M · APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex · the same entry in another collection · chain L against L, TM-score 1.00

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 Q13564
Every structure of UniProt Q8TBC4
Every structure of UniProt Q15843
Elsewhere: RCSB PDB 1R4M · PDBe 1R4M · UniProt Q13564 · UniProt Q8TBC4 · UniProt Q15843

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