MolNFT v1 · #176167 · protein

Crystal structure of PENA39 beta-lactamase

7DDM: “Crystal structure of PENA39 beta-lactamase”. X-ray diffraction, 1 pocket (best druggability 0.31). MolNFT v1 #176167 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DDM
Type: protein
Length: 271 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase; Ala-ala-arg-asp-ala-ala-val-ser-asp-ala-ala-ala
EC: 3.5.2.6
UniProt: B9BS30
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	259	44% helix, 18% strand	B9BS30
E	Ala-ala-arg-asp-ala-ala-val-ser-asp-ala-ala-ala	protein	12	67% helix, 0% strand	—

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A
ACT · Acetate ion · additive · 3 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	71	0.31	0.74	15	MPD, ACT

Interfaces

1 interface between chains.

A–E · 261 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

7DDM · Crystal Structure of PenA39 beta-Lactamase · 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 B9BS30
Elsewhere: RCSB PDB 7DDM · PDBe 7DDM · UniProt B9BS30

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