MolNFT v1 · #59450 · protein

Crystal structure of beta-lactamase oxy-1-1 from klebsiella oxytoca

3BYD: “Crystal structure of beta-lactamase oxy-1-1 from klebsiella oxytoca”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.38). MolNFT v1 #59450 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BYD
Type: protein
Length: 261 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase oxy-1
EC: 3.5.2.6
UniProt: P22391
Ligands: SO4
Pockets: 1 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase oxy-1 (EC 3.5.2.6)	protein	261	43% helix, 18% strand	P22391

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A
ACT · Acetate ion · additive · 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	107	0.38	0.75	22	SO4

Compared structures

3BYD · Crystal structure of beta-lactamase OXY-1-1 from Klebsiella oxytoca · the same entry in another collection · chain A against A, TM-score 1.00
P22391 · AlphaFold monomer V2.0 prediction for beta-lactamase oxy-1 (P22391) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P22391
Elsewhere: RCSB PDB 3BYD · PDBe 3BYD · UniProt P22391

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