MolNFT v1 · #120105 · protein

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

5GPE · Transcriptional regulator, merr-family: “Crystal structure of the transcription regulator PBRR691 from ralstonia metallidurans CH34 in complex with…”. X-ray diffraction, 1 ligand (PB), 7 pockets (best druggability 0.87). MolNFT v1…

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

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