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Structure of the peroxisomal retro-translocon formed by a heterotrimeric ubiquitin ligase complex
Analyse Structure of the peroxisomal retro-translocon formed by a heterotrimeric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 2725 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1605 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 977 Ų buried · 8 hydrogen bonds · protein-protein
- B–H · 746 Ų 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
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