MolNFT v1 · #84291 · protein

Crystal structure of penicillin-binding protein 4 from listeria monocytogenes in the apo form

3ZG7: “Crystal structure of penicillin-binding protein 4 from listeria monocytogenes in the apo form”. X-ray diffraction, 4 pockets (best druggability 0.51). MolNFT v1 #84291 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZG7
Type: protein
Length: 497 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Penicillin-binding protein 4
UniProt: Q8Y547
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Penicillin-binding protein 4	protein	40	28% helix, 23% strand	Q8Y547
B	Penicillin-binding protein 4	protein	457	42% helix, 17% strand	Q8Y547

Ligands and binding sites

TLA · L(+)-tartaric acid · additive · chains B
GOL · Glycerol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.51	0.82	26	empty
2	209	0.48	0.75	33	TLA
3	143	0.42	0.75	25	empty
4	83	0.35	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 1775 Å² buried · 24 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 modified (engineered).

Compared structures

3ZG7 · Crystal Structure of Penicillin-Binding Protein 4 from Listeria monocytogenes in the apo… · 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 Q8Y547
Elsewhere: RCSB PDB 3ZG7 · PDBe 3ZG7 · UniProt Q8Y547

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