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Crystal structure of beta-lactamse PENP_E166S in complex with meropenem

Analyse Crystal structure of beta-lactamse PENP_E166S in complex with meropenem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4N9L
Type: protein
Length: 512 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: P00808
Ligands: DWZ
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Beta-lactamase (EC 3.5.2.6)	protein	256	43% helix, 19% strand	P00808

Ligands and binding sites

DWZ · (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · 2 copies · chains B, A

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

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	810	0.72	0.78	77	empty
2	249	0.49	0.74	30	empty
3	72	0.47	0.83	18	empty
4	70	0.46	0.83	17	empty
5	75	0.33	0.75	19	DWZ

Interfaces

1 interface between chains.

B–A · 621 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

4N9L · crystal structure of beta-lactamse PenP_E166S in complex with meropenem · the same entry in another collection · chain B against B, TM-score 1.00
P00808 · AlphaFold monomer V2.0 prediction for beta-lactamase (P00808) · a predicted model of the same protein · chain B 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 P00808
Elsewhere: RCSB PDB 4N9L · PDBe 4N9L · UniProt P00808

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