Research workbench

Crystal structure of the transcription regulator PBRR691 from ralstonia metallidurans CH34 in complex with LEAD(II)

Analyse Crystal structure of the transcription regulator PBRR691 from ralstonia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GPE
Type: protein
Length: 1,009 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcriptional regulator, merr-family
UniProt: Q1LKZ5
Ligands: PB
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transcriptional regulator, merr-family	protein	123	69% helix, 3% strand	Q1LKZ5
B	Transcriptional regulator, merr-family	protein	124	69% helix, 3% strand	Q1LKZ5
C, H	Transcriptional regulator, merr-family	protein	128	69% helix, 5% strand	Q1LKZ5
D, G	Transcriptional regulator, merr-family	protein	129	66% helix, 8% strand	Q1LKZ5
E	Transcriptional regulator, merr-family	protein	122	70% helix, 3% strand	Q1LKZ5
F	Transcriptional regulator, merr-family	protein	126	67% helix, 5% strand	Q1LKZ5

Ligands and binding sites

PB · Lead (II) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

7 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	1114	0.87	0.88	131	empty
2	528	0.81	0.88	68	empty
3	445	0.80	0.88	55	empty
4	207	0.62	0.82	26	empty
5	119	0.58	0.85	22	empty

Interfaces

16 interfaces between chains.

C–D · 2253 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 2211 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 2202 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 2166 Å² buried · 24 hydrogen bonds · protein-protein
B–G · 877 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

5GPE · Crystal structure of the transcription regulator PbrR691 from Ralstonia metallidurans… · 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 Q1LKZ5
Elsewhere: RCSB PDB 5GPE · PDBe 5GPE · UniProt Q1LKZ5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.