Research workbench
Mechanism of farnesylated caax protein processing by the integral membrane protease RCE1
Analyse Mechanism of farnesylated caax protein processing by the integral membrane… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CAD
- Type
- protein
- Length
- 2,737 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment light chain; Antibody Fab fragment heavy chain; RAS and a-factor…
- UniProt
- Q6LZY8
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 43% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Antibody Fab fragment light chain | protein | 211 | 6% helix, 52% strand | — |
| B | Antibody Fab fragment heavy chain | protein | 221 | 8% helix, 52% strand | — |
| C | RAS and a-factor converting enzyme 1, RCE1 | protein | 251 | 82% helix, 0% strand | Q6LZY8 |
| E | Antibody Fab fragment heavy chain | protein | 220 | 5% helix, 53% strand | — |
| F | RAS and a-factor converting enzyme 1, RCE1 | protein | 250 | 83% helix, 0% strand | Q6LZY8 |
| G, J | Antibody Fab fragment light chain | protein | 212 | 6% helix, 52% strand | — |
| H, K | Antibody Fab fragment heavy chain | protein | 221 | 4% helix, 52% strand | — |
| I | RAS and a-factor converting enzyme 1, RCE1 | protein | 254 | 83% helix, 1% strand | Q6LZY8 |
| L | RAS and a-factor converting enzyme 1, RCE1 | protein | 253 | 81% helix, 1% strand | Q6LZY8 |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 2 copies · chains C, F
- LMT · Dodecyl-beta-D-maltoside · additive · 2 copies · chains I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.80 | 0.81 | 66 | empty |
| 2 | 1060 | 0.80 | 0.81 | 66 | empty |
| 3 | 1010 | 0.80 | 0.81 | 55 | empty |
| 4 | 953 | 0.79 | 0.81 | 52 | empty |
| 5 | 943 | 0.74 | 0.77 | 81 | empty |
Interfaces
18 interfaces between chains.
- G–H · 1887 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1874 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1862 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1856 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 858 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4CAD · Mechanism of farnesylated CAAX protein processing by the integral membrane protease Rce1 · 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 Q6LZY8
- Elsewhere: RCSB PDB 4CAD · PDBe 4CAD · UniProt Q6LZY8
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