Research workbench
Yeast delta-cop-I mu-homology domain complexed with GCS1 wxxf peptide
Analyse Yeast delta-cop-I mu-homology domain complexed with GCS1 wxxf peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FJX
- Type
- protein
- Length
- 797 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coatomer subunit delta; ADP-ribosylation factor GTPase-activating protein GCS1
- UniProt
- P43621, P35197
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Coatomer subunit delta | protein | 262 | 6% helix, 51% strand | P43621 |
| D | ADP-ribosylation factor GTPase-activating protein GCS1 | protein | 6 | 0% helix, 0% strand | P35197 |
| E | ADP-ribosylation factor GTPase-activating protein GCS1 | protein | 5 | 0% helix, 0% strand | P35197 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.73 | 0.77 | 91 | empty |
| 2 | 865 | 0.68 | 0.74 | 74 | empty |
| 3 | 163 | 0.49 | 0.78 | 17 | empty |
| 4 | 73 | 0.31 | 0.74 | 13 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1082 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 425 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 366 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 5FJX · Yeast delta-COP-I mu-homology domain complexed with Gcs1 WxxF peptide · the same entry in another collection · chain C against C, TM-score 1.00
- P43621 · AlphaFold monomer V2.0 prediction for coatomer subunit delta (P43621) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P35197 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor GTPase- activating protein… · a predicted model of the same protein · chain E against A, TM-score 0.79
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 P35197
- Elsewhere: RCSB PDB 5FJX · PDBe 5FJX · UniProt P43621 · UniProt P35197
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