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Crystal structure of the inhibitor NXL104 covalent adduct with tb B- lactamase

Analyse Crystal structure of the inhibitor NXL104 covalent adduct with tb B- lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DF6
Type: protein
Length: 265 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: P0C5C1
Ligands: NXL, PO4
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	265	45% helix, 16% strand	P0C5C1

Ligands and binding sites

NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	108	0.38	0.75	20	PO4, NXL

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4DF6 · Crystal Structure of the inhibitor NXL104 Covalent Adduct with TB B-lactamase · 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 P0C5C1
Elsewhere: RCSB PDB 4DF6 · PDBe 4DF6 · UniProt P0C5C1

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