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Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.

Analyse Structure of TRMBL2, an archaeal chromatin protein, shows a novel mode of DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BQT
Type: protein
Length: 1,038 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative hth-type transcriptional regulator TRMBL2
UniProt: Q8U3H1
Ligands: CA
Pockets: 15 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative hth-type transcriptional regulator TRMBL2	protein	261	53% helix, 18% strand	Q8U3H1
B	Putative hth-type transcriptional regulator TRMBL2	protein	253	54% helix, 17% strand	Q8U3H1
C, D	Putative hth-type transcriptional regulator TRMBL2	protein	262	52% helix, 17% strand	Q8U3H1

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains B, 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	411	0.67	0.80	63	empty
2	258	0.63	0.81	43	empty
3	460	0.62	0.76	51	empty
4	260	0.56	0.77	33	empty
5	124	0.54	0.82	29	empty

Interfaces

6 interfaces between chains.

B–D · 2873 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 2859 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1434 Å² buried · 15 hydrogen bonds · protein-protein
B–C · 1345 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 727 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5BQT · Structure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding. · the same entry in another collection · chain A against A, 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 C 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 5BQT · PDBe 5BQT · UniProt Q8U3H1

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