MolNFT v1 · #158085 · protein

Crystal structure of beta-lactamase from sulfitobacter sp. ee-36

6NJK: “Crystal structure of beta-lactamase from sulfitobacter sp. ee-36”. X-ray diffraction, 7 pockets (best druggability 0.71). MolNFT v1 #158085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NJK
Type: protein
Length: 725 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-lactamase
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-lactamase	protein	362	41% helix, 21% strand	—
B	Beta-lactamase	protein	363	42% helix, 21% strand	—

Ligands and binding sites

ACT · Acetate ion · additive · chains A

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

Pockets

7 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	759	0.71	0.77	62	empty
2	349	0.63	0.79	47	empty
3	223	0.55	0.78	27	empty
4	110	0.40	0.76	20	empty
5	75	0.37	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 976 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

6NJK · Crystal structure of beta-lactamase from Sulfitobacter sp. EE-36 · 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
Elsewhere: RCSB PDB 6NJK · PDBe 6NJK

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