MolNFT v1 · #89057 · protein

Ctx-M-9 class a beta-lactamase complexed with compound 10

4DDY: “Ctx-M-9 class a beta-lactamase complexed with compound 10”. X-ray diffraction, 1 ligand (DN6), 2 pockets (best druggability 0.35). MolNFT v1 #89057 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4DDY
Type: protein
Length: 521 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: Q9L5C8
Ligands: DN6
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	260	43% helix, 19% strand	Q9L5C8
B	Beta-lactamase (EC 3.5.2.6)	protein	261	44% helix, 19% strand	Q9L5C8

Ligands and binding sites

DN6 · N-[3-(1H-tetrazol-5-yl)phenyl]-3-(trifluoromethyl)benzamide · ligand · 12 copies · chains A, B
DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B

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	102	0.35	0.74	21	DN6
2	85	0.33	0.74	21	DN6

Interfaces

1 interface between chains.

A–B · 35 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4DDY · CTX-M-9 class A beta-lactamase complexed with compound 10 · 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 Q9L5C8
Elsewhere: RCSB PDB 4DDY · PDBe 4DDY · UniProt Q9L5C8

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