MolNFT v1 · #75454 · protein

Crystal structure of the transcriptional repressor bigr from xylella fastidiosa

3PQK · Biofilm growth-associated repressor: “Crystal structure of the transcriptional repressor bigr from xylella fastidiosa”. X-ray diffraction, 8 pockets (best druggability 0.72). MolNFT v1 #75454 on GenesisL1: 3D structure, binding…

PDB: 3PQK
Type: protein
Length: 603 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biofilm growth-associated repressor
UniProt: Q9PFB1
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Biofilm growth-associated repressor	protein	99	62% helix, 9% strand	Q9PFB1
B, C, D, E	Biofilm growth-associated repressor	protein	101	62% helix, 9% strand	Q9PFB1
F	Biofilm growth-associated repressor	protein	100	62% helix, 9% strand	Q9PFB1

Pockets

8 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	317	0.72	0.85	36	empty
2	294	0.66	0.82	39	empty
3	121	0.54	0.82	19	empty
4	125	0.54	0.82	20	empty
5	117	0.52	0.81	20	empty

Interfaces

6 interfaces between chains.

C–D · 1340 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 1322 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 1216 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 590 Å² buried · 10 hydrogen bonds · protein-protein
B–E · 544 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 modified (disulfide, engineered).

Compared structures

3PQK · Crystal Structure of the transcriptional repressor BigR from Xylella fastidiosa · the same entry in another collection · chain F against F, TM-score 1.00
Q9PFB1 · AlphaFold monomer V2.0 prediction for biofilm growth-associated repressor (Q9PFB1) · a predicted model of the same protein · chain C against A, TM-score 0.83

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 Q9PFB1
Elsewhere: RCSB PDB 3PQK · PDBe 3PQK · UniProt Q9PFB1

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