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Crystal structure of pgrp-S complexed with myristic acid at 2.28 a resolution

Analyse Crystal structure of pgrp-S complexed with myristic acid at 2.28 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3USX
Type: protein
Length: 684 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptidoglycan recognition protein 1
UniProt: Q9GK12
Ligands: MYR
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Peptidoglycan recognition protein 1	protein	171	28% helix, 19% strand	Q9GK12

Ligands and binding sites

MYR · Myristic acid · ligand · chains A, B, D
GOL · Glycerol · additive · chains C, D

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

Pockets

2 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	1189	0.82	0.83	137	MYR, GOL
2	153	0.60	0.83	39	empty

Interfaces

5 interfaces between chains.

A–B · 805 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 528 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 347 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 94 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 84 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3USX · Crystal structure of PGRP-S complexed with Myristic Acid at 2.28 A resolution · the same entry in another collection · chain A against A, TM-score 1.00
Q9GK12 · AlphaFold monomer V2.0 prediction for peptidoglycan recognition protein 1 (Q9GK12) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9GK12
Elsewhere: RCSB PDB 3USX · PDBe 3USX · UniProt Q9GK12

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