MolNFT v1 · #58834 · protein

Crystal structure of the class a beta-lactamase sed-1 from citrobacter sedlakii

3BFE · Class a beta-lactamase SED1: “Crystal structure of the class a beta-lactamase sed-1 from citrobacter sedlakii”. X-ray diffraction, 1 ligand (SCN), 6 pockets (best druggability 0.77). MolNFT v1 #58834 on GenesisL1: 3D structure…

PDB: 3BFE
Type: protein
Length: 1,048 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Class a beta-lactamase SED1
EC: 3.5.2.6
UniProt: Q93PQ0
Ligands: SCN
Pockets: 6 · best druggability 0.77

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Class a beta-lactamase SED1 (EC 3.5.2.6)	protein	262	43% helix, 19% strand	Q93PQ0

Ligands and binding sites

SCN · Thiocyanate ion · ion · chains 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1147	0.77	0.79	116	empty
2	396	0.73	0.84	58	empty
3	459	0.66	0.79	47	empty
4	140	0.45	0.77	22	empty
5	150	0.42	0.75	28	empty

Interfaces

4 interfaces between chains.

C–D · 546 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 536 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 357 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 76 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3BFE · Crystal Structure of the Class A beta-lactamase SED-1 from Citrobacter sedlakii · 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 Q93PQ0
Elsewhere: RCSB PDB 3BFE · PDBe 3BFE · UniProt Q93PQ0

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