MolNFT v1 · #104160 · protein

Ensemble refinement of PLU4264 protein from photorhabdus luminescens

4Q29: “Ensemble refinement of PLU4264 protein from photorhabdus luminescens”. X-ray diffraction, 2 ligands (NI, NA), 2 pockets (best druggability 0.63). MolNFT v1 #104160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q29
Type: protein
Length: 241 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PLU4264 protein
UniProt: Q7MZL9
Ligands: NI, NA
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	PLU4264 protein	protein	121	13% helix, 47% strand	Q7MZL9
B	PLU4264 protein	protein	120	10% helix, 48% strand	Q7MZL9

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · chains A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	108	0.63	0.88	23	empty
2	121	0.62	0.87	19	empty

Interfaces

1 interface between chains.

A–B · 1922 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

4Q29 · Ensemble Refinement of plu4264 protein from Photorhabdus luminescens · 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 Q7MZL9
Elsewhere: RCSB PDB 4Q29 · PDBe 4Q29 · UniProt Q7MZL9

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