MolNFT v1 · #72598 · protein

Crystal structure of blac-E166A covalently bound with cephalotin

3NDE · Beta-lactamase: “Crystal structure of blac-E166A covalently bound with cephalotin”. X-ray diffraction, 2 ligands (9EP, PO4), 1 pocket (best druggability 0.45). MolNFT v1 #72598 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 3NDE
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: 9EP, PO4
Pockets: 1 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	265	46% helix, 17% strand	P0C5C1

Ligands and binding sites

9EP · (2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid · 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	120	0.45	0.78	22	PO4, 9EP

Modifications

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

Compared structures

3NDE · Crystal Structure of BlaC-E166A covalently bound with Cephalotin · 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 3NDE · PDBe 3NDE · UniProt P0C5C1

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