MolNFT v1 · #140031 · protein + DNA

Crystal structure of CBNR_DBD-DNA complex

5XXP · Lysr-type regulatory protein: “Crystal structure of CBNR_DBD-DNA complex”. X-ray diffraction, 5 pockets (best druggability 0.39). MolNFT v1 #140031 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XXP
Type: protein + DNA
Length: 224 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr-type regulatory protein; DNA (25-mer)
UniProt: Q9WXC7
Pockets: 5 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 74% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysr-type regulatory protein	protein	87	74% helix, 7% strand	Q9WXC7
E	DNA (25-mer)	dna	25	—	—
F	DNA (25-mer)	dna	25	—	—

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	141	0.39	0.74	20	empty
2	64	0.30	0.75	14	empty
3	55	0.26	0.73	11	empty
4	56	0.25	0.73	11	empty
5	52	0.25	0.73	11	empty

Interfaces

6 interfaces between chains.

E–F · 1112 Å² buried · 102 hydrogen bonds · nucleic-nucleic
A–B · 978 Å² buried · 7 hydrogen bonds · protein-protein
A–F · 441 Å² buried · 7 hydrogen bonds · protein-nucleic
B–E · 440 Å² buried · 7 hydrogen bonds · protein-nucleic
A–E · 437 Å² buried · 10 hydrogen bonds · protein-nucleic

Compared structures

5XXP · Crystal structure of CbnR_DBD-DNA complex · 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 Q9WXC7
Elsewhere: RCSB PDB 5XXP · PDBe 5XXP · UniProt Q9WXC7

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