MolNFT v1 · #188040 · protein

Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase complex

7T92 · Peroxin-12: “Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase complex”. Electron microscopy, 3 ligands (LBN, CLR, ZN), 14 pockets (best druggability 0.76). MolNFT v1 #188040 on GenesisL1: 3D…

PDB: 7T92
Type: protein
Length: 1,159 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peroxin-12; Peroxin-2; Peroxin-10; Fab heavy chain; Fab light chain
UniProt: G2Q5N0, G2Q1C9, G2Q0E2
Ligands: LBN, CLR, ZN
Pockets: 14 · best druggability 0.76

Structure

electron microscopy · 5 distinct chains · 46% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Peroxin-12	protein	360	55% helix, 8% strand	G2Q5N0
A	Peroxin-2	protein	298	56% helix, 8% strand	G2Q1C9
C	Peroxin-10	protein	317	50% helix, 8% strand	G2Q0E2
H	Fab heavy chain	protein	88	3% helix, 50% strand	—
L	Fab light chain	protein	96	3% helix, 46% strand	—

Ligands and binding sites

LBN · 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine · ligand · 15 copies · chains B, A, C
CLR · Cholesterol · ligand · 5 copies · chains A, C
ZN · Zinc ion · metal · 5 copies · chains B, A, C

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	722	0.76	0.81	56	empty
2	918	0.75	0.79	81	LBN
3	493	0.70	0.80	44	empty
4	530	0.67	0.78	50	empty
5	736	0.67	0.75	73	empty

Interfaces

6 interfaces between chains.

B–A · 2881 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 2725 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 1605 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 977 Å² buried · 8 hydrogen bonds · protein-protein
B–H · 746 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

7T92 · Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase… · the same entry in another collection · chain B against B, 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 G2Q5N0
Every structure of UniProt G2Q1C9
Every structure of UniProt G2Q0E2
Elsewhere: RCSB PDB 7T92 · PDBe 7T92 · UniProt G2Q5N0 · UniProt G2Q1C9 · UniProt G2Q0E2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.