MolNFT v1 · #160642 · protein

Structure of cefotaxime-cdd-1 beta-lactamase complex

6PQC: “Structure of cefotaxime-cdd-1 beta-lactamase complex”. X-ray diffraction, 2 ligands (CEF, SO4), 2 pockets (best druggability 0.42). MolNFT v1 #160642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6PQC
Type: protein
Length: 252 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: A0A160YKM3
Ligands: CEF, SO4
Pockets: 2 · best druggability 0.42

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	252	37% helix, 21% strand	A0A160YKM3

Ligands and binding sites

CEF · CEFOTAXIME, C3' cleaved, open, bound form · ligand · chains A
SO4 · Sulfate ion · ion · 7 copies · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A

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

Pockets

2 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	159	0.42	0.74	28	CEF
2	55	0.32	0.77	12	empty

Modifications

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

Compared structures

6PQC · Structure of cefotaxime-CDD-1 beta-lactamase complex · 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 A0A160YKM3
Elsewhere: RCSB PDB 6PQC · PDBe 6PQC · UniProt A0A160YKM3

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