MolNFT v1 · #135523 · protein + DNA
Structure of PNOB8 para bound to nonspecific DNA
5U1J · Uncharacterized protein: “Structure of PNOB8 para bound to nonspecific DNA”. X-ray diffraction, 1 ligand (ANP), 15 pockets (best druggability 0.82). MolNFT v1 #135523 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U1J
- Type
- protein + DNA
- Length
- 1,201 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; DNA (5'- D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP…
- UniProt
- O93708
- Ligands
- ANP
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Uncharacterized protein | protein | 291 | 40% helix, 17% strand | O93708 |
| A | Uncharacterized protein | protein | 289 | 40% helix, 17% strand | O93708 |
| C | Uncharacterized protein | protein | 288 | 40% helix, 16% strand | O93708 |
| D | Uncharacterized protein | protein | 291 | 40% helix, 18% strand | O93708 |
| U | DNA (5'- D(*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*AP*TP*GP*AP*CP*AP*CP*G)- 3') | dna | 21 | — | — |
| W | DNA (5'- D(*CP*GP*TP*GP*TP*AP*AP*TP*GP*AP*CP*GP*CP*CP*GP*GP*CP*GP*TP*CP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 4 copies · chains B, C, A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.82 | 0.83 | 77 | ANP |
| 2 | 614 | 0.76 | 0.82 | 64 | ANP |
| 3 | 593 | 0.74 | 0.81 | 66 | empty |
| 4 | 427 | 0.67 | 0.79 | 49 | empty |
| 5 | 411 | 0.67 | 0.79 | 48 | empty |
Interfaces
11 interfaces between chains.
- A–D · 1973 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1940 Ų buried · 20 hydrogen bonds · protein-protein
- U–W · 949 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- B–A · 231 Ų buried · 2 hydrogen bonds · protein-protein
- B–W · 187 Ų buried · 2 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 7 covalent (covalent ligand).
Compared structures
- 5U1J · Structure of pNOB8 ParA bound to nonspecific DNA · the same entry in another collection · chain B against B, 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 O93708
- Elsewhere: RCSB PDB 5U1J · PDBe 5U1J · UniProt O93708
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