MolNFT v1 · #106121 · protein

Pcpr inducer binding domain (complex with 2,4,6-trichlorophenol)

4RPO · Pcp degradation transcriptional activation protein: “Pcpr inducer binding domain (complex with 2,4,6-trichlorophenol)”. X-ray diffraction, 1 ligand (T6C), 14 pockets (best druggability 0.73). MolNFT v1 #106121 on GenesisL1: 3D…

PDB: 4RPO
Type: protein
Length: 873 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pcp degradation transcriptional activation protein
UniProt: P52679
Ligands: T6C
Pockets: 14 · best druggability 0.73

Structure

x-ray diffraction · 3 distinct chains · 39% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pcp degradation transcriptional activation protein	protein	219	38% helix, 26% strand	P52679
C	Pcp degradation transcriptional activation protein	protein	217	39% helix, 25% strand	P52679
D	Pcp degradation transcriptional activation protein	protein	218	38% helix, 26% strand	P52679

Ligands and binding sites

T6C · 2,4,6-trichlorophenol · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · chains C, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.73	0.98	21	T6C
2	68	0.73	0.97	19	T6C
3	59	0.72	0.98	18	T6C
4	57	0.71	0.97	19	T6C
5	202	0.56	0.79	34	GOL

Interfaces

4 interfaces between chains.

A–B · 2136 Å² buried · 36 hydrogen bonds · protein-protein
C–D · 2100 Å² buried · 43 hydrogen bonds · protein-protein
B–D · 484 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 57 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4RPO · PcpR inducer binding domain (Complex with 2,4,6-trichlorophenol) · the same entry in another collection · chain A against A, TM-score 1.00
P52679 · AlphaFold monomer V2.0 prediction for pcp degradation transcriptional activation protein… · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P52679
Elsewhere: RCSB PDB 4RPO · PDBe 4RPO · UniProt P52679

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