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Cdd-1 beta-lactamase in IMIDAZOLE/MPD 5 minute avibactam complex

Analyse Cdd-1 beta-lactamase in IMIDAZOLE/MPD 5 minute avibactam complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MED
Type: protein
Length: 250 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: NXL, SO4, CO2
Pockets: 1 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	250	38% helix, 21% strand	A0A160YKM3

Ligands and binding sites

NXL · (2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide · ligand · chains A
SO4 · Sulfate ion · ion · 4 copies · chains A
CO2 · Carbon dioxide · ion · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · 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	171	0.43	0.74	30	NXL

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, carboxylation).

Compared structures

7MED · CDD-1 beta-lactamase in imidazole/MPD 5 minute avibactam 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 7MED · PDBe 7MED · UniProt A0A160YKM3

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