MolNFT v1 · #109559 · protein

Crystal structure of OP0595 complexed with ampc

4X68 · Beta-lactamase: “Crystal structure of OP0595 complexed with ampc”. X-ray diffraction, 2 ligands (OP0, NI), 8 pockets (best druggability 0.81). MolNFT v1 #109559 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4X68
Type: protein
Length: 714 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: P24735
Ligands: OP0, NI
Pockets: 8 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Beta-lactamase (EC 3.5.2.6)	protein	357	42% helix, 23% strand	P24735

Ligands and binding sites

OP0 · (2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy) amino]piperidine-2-carboxamide · ligand · 2 copies · chains A, B
NI · Nickel (II) ion · metal · 2 copies · chains A, B

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

Pockets

8 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	722	0.81	0.85	83	OP0
2	284	0.59	0.79	42	OP0
3	244	0.50	0.75	33	empty
4	123	0.42	0.75	20	empty
5	66	0.35	0.77	15	empty

Interfaces

1 interface between chains.

A–B · 1006 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4X68 · Crystal Structure of OP0595 complexed with AmpC · the same entry in another collection · chain A against A, TM-score 1.00
P24735 · AlphaFold monomer V2.0 prediction for beta-lactamase (P24735) · a predicted model of the same protein · 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 P24735
Elsewhere: RCSB PDB 4X68 · PDBe 4X68 · UniProt P24735

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