MolNFT v1 · #20319 · protein + DNA
The PHIX174 DNA binding protein J in two different capsid environments.
1RB8 · Capsid protein: “The PHIX174 DNA binding protein J in two different capsid environments.”. X-ray diffraction, 1 ligand (DC), 7 pockets (best druggability 0.61). MolNFT v1 #20319 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1RB8
- Type
- protein + DNA
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Major spike protein; Small core protein; DNA (5'-D(P*CP*AP*AP*A)-3')
- UniProt
- P08767, P31281, P69592
- Ligands
- DC
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Capsid protein | protein | 422 | 25% helix, 29% strand | P08767 |
| G | Major spike protein | protein | 187 | 2% helix, 49% strand | P31281 |
| J | Small core protein | protein | 26 | 0% helix, 4% strand | P69592 |
| X | DNA (5'-D(P*CP*AP*AP*A)-3') | dna | 4 | — | — |
Ligands and binding sites
- DC · 2'-deoxycytidine-5'-monophosphate · ligand · 6 copies · chains X, F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.61 | 0.78 | 39 | empty |
| 2 | 269 | 0.54 | 0.76 | 24 | empty |
| 3 | 112 | 0.35 | 0.73 | 24 | empty |
| 4 | 60 | 0.35 | 0.78 | 27 | empty |
| 5 | 70 | 0.34 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- F–J · 1208 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 214 Ų buried · 3 hydrogen bonds · protein-protein
- J–X · 175 Ų buried · 2 hydrogen bonds · protein-nucleic
- F–X · 148 Ų buried · 3 hydrogen bonds · protein-nucleic
Compared structures
- 1RB8 · The phiX174 DNA binding protein J in two different capsid environments. · the same entry in another collection · chain F against F, 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 P08767
- Every structure of UniProt P31281
- Every structure of UniProt P69592
- Elsewhere: RCSB PDB 1RB8 · PDBe 1RB8 · UniProt P08767 · UniProt P31281 · UniProt P69592
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