MolNFT v1 · #114435 · protein + DNA
Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
5BPD: “Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.”. X-ray diffraction, 16 pockets (best druggability 0.75). MolNFT v1 #114435 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5BPD
- Type
- protein + DNA
- Length
- 1,087 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRMBL2; DNA (5'- D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)- 3')…
- UniProt
- Q8U3H1
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · 6 distinct chains · 51% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRMBL2 | protein | 263 | 51% helix, 18% strand | Q8U3H1 |
| B | TRMBL2 | protein | 262 | 51% helix, 17% strand | Q8U3H1 |
| C | TRMBL2 | protein | 260 | 51% helix, 18% strand | Q8U3H1 |
| D | TRMBL2 | protein | 260 | 52% helix, 17% strand | Q8U3H1 |
| E | DNA (5'- D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)- 3') | dna | 21 | — | — |
| F | DNA (5'- D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)- 3') | dna | 21 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- IMD · Imidazole · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.75 | 0.80 | 88 | IMD |
| 2 | 633 | 0.75 | 0.81 | 75 | GOL |
| 3 | 372 | 0.70 | 0.82 | 47 | empty |
| 4 | 362 | 0.68 | 0.81 | 50 | empty |
| 5 | 81 | 0.66 | 0.92 | 18 | empty |
Interfaces
15 interfaces between chains.
- A–C · 2925 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 2882 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1481 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1458 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 963 Ų buried · 86 hydrogen bonds · nucleic-nucleic
Compared structures
- 5BPD · Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding. · the same entry in another collection · chain F against F, 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 D against A, TM-score 0.81
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 5BPD · PDBe 5BPD · UniProt Q8U3H1
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