MolNFT v1 · #119036 · protein
Yeast delta-cop-I mu-homology domain complexed with DSL1 wxwxv peptide
5FJZ · Coatomer subunit delta: “Yeast delta-cop-I mu-homology domain complexed with DSL1 wxwxv peptide”. X-ray diffraction, 12 pockets (best druggability 0.70). MolNFT v1 #119036 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5FJZ
- Type
- protein
- Length
- 1,070 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coatomer subunit delta; Protein transport protein DSL1
- UniProt
- P43621, P53847
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Coatomer subunit delta | protein | 262 | 8% helix, 48% strand | P43621 |
| B | Coatomer subunit delta | protein | 260 | 7% helix, 47% strand | P43621 |
| P, Q, R, S | Protein transport protein DSL1 | protein | 6 | 0% helix, 0% strand | P53847 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.70 | 0.77 | 87 | empty |
| 2 | 485 | 0.65 | 0.77 | 53 | empty |
| 3 | 346 | 0.64 | 0.79 | 40 | empty |
| 4 | 219 | 0.61 | 0.82 | 26 | empty |
| 5 | 230 | 0.60 | 0.81 | 42 | empty |
Interfaces
13 interfaces between chains.
- C–D · 1118 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1106 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1072 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1047 Ų buried · 19 hydrogen bonds · protein-protein
- D–S · 530 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5FJZ · Yeast delta-COP-I mu-homology domain complexed with Dsl1 WxWxV peptide · the same entry in another collection · chain S against S, TM-score 1.00
- P43621 · AlphaFold monomer V2.0 prediction for coatomer subunit delta (P43621) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P43621
- Every structure of UniProt P53847
- Elsewhere: RCSB PDB 5FJZ · PDBe 5FJZ · UniProt P43621 · UniProt P53847
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.