MolNFT v1 · #16944 · protein

Cephalosporin C deacetylase from bacillus subtilis

1ODS: “Cephalosporin C deacetylase from bacillus subtilis”. X-ray diffraction, 2 ligands (MG, CL), 20 pockets (best druggability 0.78). MolNFT v1 #16944 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ODS
Type: protein
Length: 2,528 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cephalosporin C deacetylase
EC: 3.1.1.41
UniProt: P94388
Ligands: MG, CL
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cephalosporin C deacetylase (EC 3.1.1.41)	protein	316	38% helix, 21% strand	P94388

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, D
CL · Chloride ion · ion · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.78	0.80	110	empty
2	1044	0.77	0.79	92	empty
3	957	0.77	0.79	86	empty
4	1035	0.75	0.78	85	empty
5	143	0.67	0.88	24	MG

Interfaces

17 interfaces between chains.

C–H · 1259 Å² buried · 36 hydrogen bonds · protein-protein
E–G · 1249 Å² buried · 32 hydrogen bonds · protein-protein
D–F · 1247 Å² buried · 33 hydrogen bonds · protein-protein
E–F · 942 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 938 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

1ODS · Cephalosporin C deacetylase from Bacillus subtilis · the same entry in another collection · chain H against H, TM-score 1.00
P94388 · AlphaFold monomer V2.0 prediction for cephalosporin-C deacetylase (P94388) · a predicted model of the same protein · 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 P94388
Elsewhere: RCSB PDB 1ODS · PDBe 1ODS · UniProt P94388

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