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Crystal structure of dim-1 metallo-beta-lactamase exposed to ceftazidime

Analyse Crystal structure of dim-1 metallo-beta-lactamase exposed to ceftazidime in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZEJ
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Metallo-beta-lactamase
UniProt: D5JGF6
Ligands: ZN, CL
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Metallo-beta-lactamase	protein	219	27% helix, 31% strand	D5JGF6

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
CL · Chloride ion · ion · 10 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.57	0.75	42	empty
2	197	0.51	0.77	26	ZN, CL
3	167	0.51	0.78	21	ZN, CL
4	145	0.48	0.78	30	CL

Interfaces

1 interface between chains.

A–B · 237 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4ZEJ · Crystal Structure of DIM-1 Metallo-beta-Lactamase exposed to Ceftazidime · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt D5JGF6
Elsewhere: RCSB PDB 4ZEJ · PDBe 4ZEJ · UniProt D5JGF6

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