Research workbench
Crystal structure of 60-mer bfdv capsid protein in complex with single stranded DNA
Analyse Crystal structure of 60-mer bfdv capsid protein in complex with single stranded… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J37
- Type
- protein + DNA
- Length
- 1,045 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beak and feather disease virus capsid protein; Single stranded DNA
- UniProt
- A0A023R6W2
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, B, C, D | Beak and feather disease virus capsid protein | protein | 206 | 8% helix, 45% strand | A0A023R6W2 |
| F, G, H, I, J | Single stranded DNA | dna | 3 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 5 copies · chains E, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.55 | 0.85 | 21 | empty |
| 2 | 97 | 0.53 | 0.84 | 22 | empty |
| 3 | 90 | 0.53 | 0.84 | 20 | empty |
| 4 | 78 | 0.53 | 0.85 | 20 | empty |
| 5 | 113 | 0.52 | 0.82 | 24 | empty |
Interfaces
15 interfaces between chains.
- B–D · 1061 Ų buried · 20 hydrogen bonds · protein-protein
- E–B · 1052 Ų buried · 18 hydrogen bonds · protein-protein
- E–A · 1050 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1041 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1038 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5J37 · Crystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA · the same entry in another collection · chain E against E, 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 A0A023R6W2
- Elsewhere: RCSB PDB 5J37 · PDBe 5J37 · UniProt A0A023R6W2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.