MolNFT v1 · #114421 · protein + DNA
Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
5BOX · Putative hth-type transcriptional regulator TRMBL2: “Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.”. X-ray diffraction, 17 pockets (best druggability 0.79). MolNFT v1 #114421 on GenesisL1: 3D…
- PDB
- 5BOX
- Type
- protein + DNA
- Length
- 1,102 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative hth-type transcriptional regulator TRMBL2; DNA tgm (25-mer); DNA (25-mer)
- UniProt
- Q8U3H1
- Pockets
- 17 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Putative hth-type transcriptional regulator TRMBL2 | protein | 263 | 50% helix, 17% strand | Q8U3H1 |
| E | DNA tgm (25-mer) | dna | 25 | — | — |
| F | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, C, B, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.79 | 0.80 | 103 | empty |
| 2 | 934 | 0.79 | 0.81 | 84 | empty |
| 3 | 241 | 0.75 | 0.89 | 26 | empty |
| 4 | 257 | 0.63 | 0.81 | 30 | empty |
| 5 | 252 | 0.61 | 0.80 | 33 | empty |
Interfaces
15 interfaces between chains.
- A–C · 2936 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2913 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1474 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1448 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1111 Ų buried · 115 hydrogen bonds · nucleic-nucleic
Compared structures
- 5BOX · Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding. · the same entry in another collection · chain C against C, TM-score 1.00
- Q8U3H1 · AlphaFold monomer V2.0 prediction for putative hth-type transcriptional regulator TRMBL2… · a predicted model of the same protein · chain A against A, TM-score 0.53
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 Q8U3H1
- Elsewhere: RCSB PDB 5BOX · PDBe 5BOX · UniProt Q8U3H1
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