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Crystal structure of class C beta-lactamase

Analyse Crystal structure of class C beta-lactamase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GGW
Type: protein
Length: 717 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
EC: 3.5.2.6
UniProt: B7SNP8
Ligands: SO4, PO4
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase (EC 3.5.2.6)	protein	357	41% helix, 23% strand	B7SNP8
B	Beta-lactamase (EC 3.5.2.6)	protein	360	39% helix, 23% strand	B7SNP8

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

6 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	356	0.68	0.82	58	SO4, PO4
2	343	0.67	0.82	55	SO4, PO4
3	367	0.56	0.75	41	empty
4	170	0.49	0.77	22	empty
5	77	0.30	0.73	20	empty

Interfaces

1 interface between chains.

A–B · 709 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

5GGW · Crystal structure of Class C 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 B7SNP8
Elsewhere: RCSB PDB 5GGW · PDBe 5GGW · UniProt B7SNP8

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