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Crystal structure of rsrr complexed to a 39 basepair DNA fragment of the rsrr promoter

Analyse Crystal structure of rsrr complexed to a 39 basepair DNA fragment of the rsrr… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y42
Type: protein + DNA
Length: 390 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RRF2 family transcriptional regulator; DNA (39-mer)
UniProt: F2RGC9
Ligands: FES
Pockets: 9 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 52% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RRF2 family transcriptional regulator	protein	159	52% helix, 7% strand	F2RGC9
E	DNA (39-mer)	dna	36	—	—
F	DNA (39-mer)	dna	36	—	—

Ligands and binding sites

FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	275	0.77	0.89	29	empty
2	260	0.74	0.87	29	empty
3	204	0.66	0.85	34	empty
4	326	0.59	0.78	33	empty
5	133	0.45	0.77	15	empty

Interfaces

6 interfaces between chains.

A–B · 2296 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 1612 Å² buried · 128 hydrogen bonds · nucleic-nucleic
B–E · 571 Å² buried · 5 hydrogen bonds · protein-nucleic
A–E · 564 Å² buried · 13 hydrogen bonds · protein-nucleic
A–F · 551 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

6Y42 · Crystal Structure of RsrR complexed to a 39 basepair DNA fragment of the rsrR promoter · the same entry in another collection · chain A against A, TM-score 1.00

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 F2RGC9
Elsewhere: RCSB PDB 6Y42 · PDBe 6Y42 · UniProt F2RGC9

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