MolNFT v1 · #128016 · protein

L2 class a serine-beta-lactamase

5NE2: “L2 class a serine-beta-lactamase”. X-ray diffraction, 1 ligand (DGL), 10 pockets (best druggability 0.40). MolNFT v1 #128016 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NE2
Type: protein
Length: 540 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q9RBQ1
Ligands: DGL
Pockets: 10 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	270	47% helix, 19% strand	Q9RBQ1

Ligands and binding sites

DGL · D-glutamic acid · ligand · 2 copies · chains A, B

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

Pockets

10 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	57	0.40	0.81	14	empty
2	103	0.40	0.77	19	empty
3	97	0.40	0.76	19	empty
4	52	0.38	0.81	16	empty
5	101	0.38	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 1082 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

5NE2 · L2 class A serine-beta-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 Q9RBQ1
Elsewhere: RCSB PDB 5NE2 · PDBe 5NE2 · UniProt Q9RBQ1

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