MolNFT v1 · #151484 · protein + DNA
Arbitrium peptide receptor from spbeta phage in complex with 43 mer DNA
6HP7 · SPBC2 prophage-derived uncharacterized protein yopk: “Arbitrium peptide receptor from spbeta phage in complex with 43 mer DNA”. X-ray diffraction, 1 ligand (PO4), 15 pockets (best druggability 0.70). MolNFT v1 #151484 on GenesisL1…
- PDB
- 6HP7
- Type
- protein + DNA
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SPBC2 prophage-derived uncharacterized protein yopk; DNA (43-mer)
- UniProt
- O31927
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SPBC2 prophage-derived uncharacterized protein yopk | protein | 386 | 72% helix, 0% strand | O31927 |
| C | DNA (43-mer) | dna | 43 | — | — |
| D | DNA (43-mer) | dna | 43 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.70 | 0.78 | 59 | empty |
| 2 | 686 | 0.69 | 0.77 | 46 | empty |
| 3 | 573 | 0.65 | 0.76 | 50 | PO4 |
| 4 | 490 | 0.63 | 0.76 | 39 | empty |
| 5 | 429 | 0.62 | 0.76 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1898 Ų buried · 171 hydrogen bonds · nucleic-nucleic
- A–B · 1430 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 612 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 476 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6HP7 · ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE in complex with 43 mer DNA · the same entry in another collection · chain A against A, TM-score 1.00
- O31927 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived uncharacterized protein… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O31927
- Elsewhere: RCSB PDB 6HP7 · PDBe 6HP7 · UniProt O31927
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