MolNFT v1 · #134487 · protein + DNA
Structure of histone-based chromatin in archaea
5T5K · DNA-binding protein hmf-2: “Structure of histone-based chromatin in archaea”. X-ray diffraction, 18 pockets (best druggability 0.63). MolNFT v1 #134487 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5T5K
- Type
- protein + DNA
- Length
- 584 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein hmf-2; DNA (90-mer)
- UniProt
- P19267
- Pockets
- 18 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F | DNA-binding protein hmf-2 | protein | 67 | 73% helix, 6% strand | P19267 |
| B, C | DNA-binding protein hmf-2 | protein | 68 | 68% helix, 6% strand | P19267 |
| I | DNA (90-mer) | dna | 90 | — | — |
| J | DNA (90-mer) | dna | 90 | — | — |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 3 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.63 | 0.74 | 51 | empty |
| 2 | 386 | 0.57 | 0.75 | 23 | empty |
| 3 | 337 | 0.55 | 0.75 | 19 | empty |
| 4 | 206 | 0.55 | 0.79 | 26 | empty |
| 5 | 308 | 0.55 | 0.76 | 19 | empty |
Interfaces
20 interfaces between chains.
- I–J · 3995 Ų buried · 368 hydrogen bonds · nucleic-nucleic
- A–B · 1788 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1732 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1684 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- P19267 · AlphaFold monomer V2.0 prediction for DNA-binding protein hmf-2 (P19267) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P19267
- Elsewhere: RCSB PDB 5T5K · PDBe 5T5K · UniProt P19267
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