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Structure of rcsb from salmonella enterica serovar typhimurium bound to promoter P1FLHDC in the presence of phosphomimetic BEF3-

Analyse Structure of rcsb from salmonella enterica serovar typhimurium bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZIX
Type: protein + DNA
Length: 451 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulatory protein rcsb; P1FLHDC promoter sequence of 23 bp
UniProt: C4PCU2
Ligands: BFD, MG
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 48% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Transcriptional regulatory protein rcsb	protein	205	50% helix, 12% strand	C4PCU2
A	Transcriptional regulatory protein rcsb	protein	202	46% helix, 12% strand	C4PCU2
E	P1FLHDC promoter sequence of 23 bp	dna	22	—	—
F	P1FLHDC promoter sequence of 23 bp	dna	22	—	—

Ligands and binding sites

BFD · Aspartate beryllium trifluoride · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

8 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	857	0.75	0.79	75	MG, BFD
2	404	0.68	0.81	41	empty
3	61	0.55	0.88	18	empty
4	85	0.50	0.83	21	empty
5	164	0.49	0.77	31	empty

Interfaces

6 interfaces between chains.

E–F · 975 Å² buried · 79 hydrogen bonds · nucleic-nucleic
B–A · 892 Å² buried · 2 hydrogen bonds · protein-protein
B–E · 404 Å² buried · 5 hydrogen bonds · protein-nucleic
A–F · 377 Å² buried · 7 hydrogen bonds · protein-nucleic
B–F · 339 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6ZIX · Structure of RcsB from Salmonella enterica serovar Typhimurium bound to promoter P1flhDC… · the same entry in another collection · chain E against E, TM-score 1.00

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Every structure of UniProt C4PCU2
Elsewhere: RCSB PDB 6ZIX · PDBe 6ZIX · UniProt C4PCU2

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