MolNFT v1 · #169642 · protein

Semet-rns, in complex with potential inhibitor

6XIV · Regulatory protein rns: “Semet-rns, in complex with potential inhibitor”. X-ray diffraction, 2 ligands (DKA, LMR), 8 pockets (best druggability 0.80). MolNFT v1 #169642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6XIV
Type: protein
Length: 513 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Regulatory protein rns
UniProt: P16114
Ligands: DKA, LMR
Pockets: 8 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Regulatory protein rns	protein	257	48% helix, 16% strand	P16114
B	Regulatory protein rns	protein	256	47% helix, 17% strand	P16114

Ligands and binding sites

DKA · Decanoic acid · ligand · 2 copies · chains A, B
LMR · (2S)-2-hydroxybutanedioic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1172	0.80	0.81	94	DKA
2	386	0.75	0.84	32	DKA
3	71	0.72	0.95	19	empty
4	673	0.72	0.79	51	LMR
5	195	0.51	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 604 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 modified (engineered).

Compared structures

6XIV · SeMet-Rns, in complex with potential inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
P16114 · AlphaFold monomer V2.0 prediction for regulatory protein rns (P16114) · a predicted model of the same protein · chain B against A, TM-score 0.92

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 P16114
Elsewhere: RCSB PDB 6XIV · PDBe 6XIV · UniProt P16114

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