MolNFT v1 · #191379 · protein
AVS3 bound to phage phiv-1 terminase
8DGC · SEAVS3: “AVS3 bound to phage phiv-1 terminase”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #191379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8DGC
- Type
- protein
- Length
- 10,216 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SEAVS3; Terminase, large subunit
- EC
- 3.6.4.-, 3.1.21.-
- UniProt
- A0A7G3WWS0
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | SEAVS3 | protein | 2028 | 55% helix, 7% strand | — |
| B, D | SEAVS3 | protein | 2004 | 55% helix, 8% strand | — |
| E, F, G, H | Terminase, large subunit (EC 3.6.4.-, 3.1.21.-) | protein | 538 | 37% helix, 18% strand | A0A7G3WWS0 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.86 | 0.88 | 104 | empty |
| 2 | 817 | 0.84 | 0.86 | 96 | empty |
| 3 | 882 | 0.82 | 0.84 | 90 | empty |
| 4 | 788 | 0.80 | 0.84 | 77 | empty |
| 5 | 1117 | 0.80 | 0.81 | 94 | empty |
Interfaces
9 interfaces between chains.
- B–F · 4098 Ų buried · 33 hydrogen bonds · protein-protein
- D–H · 4092 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 3938 Ų buried · 35 hydrogen bonds · protein-protein
- C–G · 3914 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 1428 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 8DGC · Avs3 bound to phage PhiV-1 terminase · the same entry in another collection · chain A against A, 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 A0A7G3WWS0
- Elsewhere: RCSB PDB 8DGC · PDBe 8DGC · UniProt A0A7G3WWS0
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