MolNFT v1 · #191380 · protein
AVS4 bound to phage phiv-1 portal
8DGF · ATP-binding protein AVS4: “AVS4 bound to phage phiv-1 portal”. Electron microscopy, 2 ligands (ATP, MG), 20 pockets (best druggability 0.82). MolNFT v1 #191380 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 8DGF
- Type
- protein
- Length
- 7,902 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ATP-binding protein AVS4; Portal protein
- UniProt
- A0A7G3WWQ5
- Ligands
- ATP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 60% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | ATP-binding protein AVS4 | protein | 1541 | 61% helix, 7% strand | — |
| B, D | ATP-binding protein AVS4 | protein | 1534 | 62% helix, 8% strand | — |
| E, F, G, H | Portal protein | protein | 438 | 48% helix, 17% strand | A0A7G3WWQ5 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
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 | 954 | 0.82 | 0.83 | 98 | ATP, MG |
| 2 | 1074 | 0.81 | 0.82 | 119 | ATP, MG |
| 3 | 1195 | 0.81 | 0.82 | 104 | empty |
| 4 | 774 | 0.80 | 0.84 | 85 | empty |
| 5 | 819 | 0.80 | 0.83 | 69 | empty |
Interfaces
10 interfaces between chains.
- B–F · 6105 Ų buried · 62 hydrogen bonds · protein-protein
- C–G · 6092 Ų buried · 59 hydrogen bonds · protein-protein
- A–E · 6072 Ų buried · 58 hydrogen bonds · protein-protein
- D–H · 6070 Ų buried · 62 hydrogen bonds · protein-protein
- A–D · 2928 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified (disulfide, formylation).
Compared structures
- 8DGF · Avs4 bound to phage PhiV-1 portal · 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 A0A7G3WWQ5
- Elsewhere: RCSB PDB 8DGF · PDBe 8DGF · UniProt A0A7G3WWQ5
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