MolNFT v1 · #55035 · protein

Dntr inducer binding domain in complex with salicylate. monoclinic crystal form

2Y7K · Lysr-type regulatory protein: “Dntr inducer binding domain in complex with salicylate. monoclinic crystal form”. X-ray diffraction, 1 ligand (SAL), 12 pockets (best druggability 0.72). MolNFT v1 #55035 on GenesisL1: 3D structure…

PDB: 2Y7K
Type: protein
Length: 845 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysr-type regulatory protein
UniProt: Q7WT50
Ligands: SAL
Pockets: 12 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysr-type regulatory protein	protein	211	37% helix, 27% strand	Q7WT50
B	Lysr-type regulatory protein	protein	213	37% helix, 26% strand	Q7WT50
C	Lysr-type regulatory protein	protein	212	35% helix, 26% strand	Q7WT50
D	Lysr-type regulatory protein	protein	209	36% helix, 27% strand	Q7WT50

Ligands and binding sites

SAL · 2-hydroxybenzoic acid · ligand · 6 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	764	0.72	0.78	60	empty
2	61	0.71	0.97	21	empty
3	51	0.69	0.97	17	SAL
4	221	0.56	0.78	42	empty
5	58	0.45	0.83	17	empty

Interfaces

4 interfaces between chains.

C–D · 1476 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1377 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 750 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 57 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2Y7K · DntR Inducer Binding Domain in Complex with Salicylate. Monoclinic crystal form · 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 Q7WT50
Elsewhere: RCSB PDB 2Y7K · PDBe 2Y7K · UniProt Q7WT50

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