MolNFT v1 · #72950 · protein

Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) with alpha-rhamnose at 2.9 a resolution

3NNO · Peptidoglycan recognition protein 1: “Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) with alpha-rhamnose at 2.9 a…”. X-ray diffraction, 1 ligand (RAM), 4 pockets (best druggability 0.83). MolNFT v1…

PDB: 3NNO
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: RAM
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Peptidoglycan recognition protein 1	protein	171	30% helix, 20% strand	Q9GK12

Ligands and binding sites

RAM · alpha-L-rhamnopyranose · sugar · chains C, D
TLA · L(+)-tartaric acid · additive · chains C, D

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	1027	0.83	0.84	126	TLA, RAM
2	105	0.35	0.73	25	empty
3	73	0.30	0.73	17	empty
4	59	0.26	0.73	19	empty

Interfaces

5 interfaces between chains.

A–B · 796 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 519 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 355 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 124 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 84 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 12 disulfide (disulfide).

Compared structures

3NNO · Crystal structure of the complex of peptidoglycan recognition protein (PGRP-S) with… · 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 3NNO · PDBe 3NNO · UniProt Q9GK12

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