MolNFT v1 · #179055 · protein
Yeast GLO3 gap domain
7JTZ · ADP-ribosylation factor GTPase-activating protein GLO3: “Yeast GLO3 gap domain”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.71). MolNFT v1 #179055 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7JTZ
- Type
- protein
- Length
- 561 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor GTPase-activating protein GLO3
- UniProt
- P38682
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ADP-ribosylation factor GTPase-activating protein GLO3 | protein | 143 | 53% helix, 9% strand | P38682 |
| A | ADP-ribosylation factor GTPase-activating protein GLO3 | protein | 139 | 53% helix, 8% strand | P38682 |
| C | ADP-ribosylation factor GTPase-activating protein GLO3 | protein | 140 | 51% helix, 9% strand | P38682 |
| D | ADP-ribosylation factor GTPase-activating protein GLO3 | protein | 139 | 51% helix, 9% strand | P38682 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, A, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.71 | 0.80 | 51 | empty |
| 2 | 500 | 0.69 | 0.79 | 50 | empty |
| 3 | 347 | 0.64 | 0.79 | 44 | empty |
| 4 | 81 | 0.36 | 0.76 | 20 | empty |
| 5 | 54 | 0.33 | 0.77 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–A · 676 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 611 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 P38682
- Elsewhere: RCSB PDB 7JTZ · PDBe 7JTZ · UniProt P38682
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