Research workbench
Crystal structure of ARF1 bound to the GAMMA/ZETA-cop core complex
Analyse Crystal structure of ARF1 bound to the GAMMA/ZETA-cop core complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TJZ
- Type
- protein
- Length
- 1,122 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 1; Coatomer subunit gamma; Coatomer subunit zeta-1
- UniProt
- P11076, P53620, P35604
- Ligands
- GNP, MG
- Pockets
- 19 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | ADP-ribosylation factor 1 | protein | 159 | 33% helix, 26% strand | P11076 |
| B | Coatomer subunit gamma | protein | 264 | 69% helix, 0% strand | P53620 |
| C, F | Coatomer subunit zeta-1 | protein | 140 | 41% helix, 26% strand | P35604 |
| E | Coatomer subunit gamma | protein | 260 | 72% helix, 0% strand | P53620 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.86 | 0.87 | 93 | GNP, MG |
| 2 | 603 | 0.69 | 0.78 | 59 | empty |
| 3 | 584 | 0.68 | 0.77 | 52 | empty |
| 4 | 146 | 0.56 | 0.82 | 18 | empty |
| 5 | 250 | 0.51 | 0.75 | 45 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2089 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 1975 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 979 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 935 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 443 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3TJZ · Crystal Structure of Arf1 Bound to the gamma/zeta-COP Core Complex · the same entry in another collection · chain F against F, TM-score 1.00
- P35604 · AlphaFold monomer V2.0 prediction for coatomer subunit zeta-1 (P35604) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P53620 · AlphaFold monomer V2.0 prediction for coatomer subunit gamma-1 (P53620) · a predicted model of the same protein · chain E against A, TM-score 0.97
- P11076 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor 1 (P11076) · a predicted model of the same protein · chain D against A, TM-score 0.96
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 P11076
- Every structure of UniProt P53620
- Every structure of UniProt P35604
- Elsewhere: RCSB PDB 3TJZ · PDBe 3TJZ · UniProt P11076 · UniProt P53620 · UniProt P35604
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