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Penicillin G acylated BD3459 predatory endopeptidase from bdellovibrio bacteriovorus in complex with immunity protein BD3460

Analyse Penicillin G acylated BD3459 predatory endopeptidase from bdellovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5CED
Type: protein
Length: 575 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BD3459; BD3460
EC: 3.4.16.4
UniProt: Q6MHT0, Q6MHS9
Ligands: PNM
Pockets: 6 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BD3459 (EC 3.4.16.4)	protein	381	34% helix, 23% strand	Q6MHT0
B	BD3460	protein	194	54% helix, 1% strand	Q6MHS9

Ligands and binding sites

PNM · Open form - penicillin G · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	587	0.68	0.78	54	PNM
2	268	0.52	0.75	30	empty
3	122	0.48	0.80	25	empty
4	83	0.36	0.76	16	empty
5	57	0.31	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1081 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).

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 Q6MHT0
Every structure of UniProt Q6MHS9
Elsewhere: RCSB PDB 5CED · PDBe 5CED · UniProt Q6MHT0 · UniProt Q6MHS9

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