MolNFT v1 · #63875 · protein + DNA
Crystal structure of seqa bound to DNA
3FMT · Protein seqa: “Crystal structure of seqa bound to DNA”. X-ray diffraction, 12 pockets (best druggability 0.79). MolNFT v1 #63875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FMT
- Type
- protein + DNA
- Length
- 724 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein seqa; 5'-D(*GP*AP*GP*TP*CP*GP*(6MA) P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*T…
- UniProt
- P0AFY8
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Protein seqa | protein | 162 | 59% helix, 8% strand | P0AFY8 |
| B, F | Protein seqa | protein | 157 | 57% helix, 10% strand | P0AFY8 |
| C, G | 5'-D(*GP*AP*GP*TP*CP*GP*(6MA) P*TP*CP*GP*GP*CP*GP*GP*GP*(6MA)P*TP*CP*CP*TP*TP*A)-3' | dna | 22 | — | — |
| D, H | 5'-D(*TP*CP*TP*AP*AP*GP*GP*AP*TP*CP*CP*CP*GP*CP*CP*GP*AP*TP *CP*GP*AP*C)-3' | dna | 21 | — | — |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.79 | 0.81 | 83 | empty |
| 2 | 915 | 0.77 | 0.80 | 79 | empty |
| 3 | 463 | 0.61 | 0.75 | 36 | empty |
| 4 | 248 | 0.58 | 0.79 | 29 | empty |
| 5 | 132 | 0.53 | 0.81 | 15 | MPD |
Interfaces
15 interfaces between chains.
- A–B · 1552 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1551 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 938 Ų buried · 90 hydrogen bonds · nucleic-nucleic
- C–D · 937 Ų buried · 89 hydrogen bonds · nucleic-nucleic
- F–G · 587 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
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 P0AFY8
- Elsewhere: RCSB PDB 3FMT · PDBe 3FMT · UniProt P0AFY8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.