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Complex structure of lysostaphin SH3B domain with peptidoglycan fragment

Analyse Complex structure of lysostaphin SH3B domain with peptidoglycan fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LEO
Type: protein
Length: 196 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysostaphin; Gly-gly-gly-gly-gly
EC: 3.4.24.75
UniProt: P10547
Ligands: SO4
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Lysostaphin (EC 3.4.24.75)	protein	93	0% helix, 58% strand	P10547
G, H	Gly-gly-gly-gly-gly	protein	5	0% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, G
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

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

Pockets

2 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	348	0.63	0.79	33	empty
2	95	0.35	0.74	25	SO4

Interfaces

3 interfaces between chains.

A–H · 319 Å² buried · 5 hydrogen bonds · protein-protein
B–G · 306 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 209 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5LEO · Complex structure of lysostaphin SH3b domain with peptidoglycan fragment · the same entry in another collection · chain A against A, TM-score 1.00
P10547 · AlphaFold monomer V2.0 prediction for lysostaphin (P10547) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P10547
Elsewhere: RCSB PDB 5LEO · PDBe 5LEO · UniProt P10547

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