MolNFT v1 · #73920 · protein
Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) with heparin-dissacharide at 2.8 a resolution
3OGX · Peptidoglycan recognition protein 1: “Crystal structure of the complex of peptidoglycan recognition protein (pgrp-S) with heparin-dissacharide at…”. X-ray diffraction, 2 ligands (UAP, SGN), 4 pockets (best druggability 0.83). MolNFT…
- PDB
- 3OGX
- 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
- UAP, SGN
- 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
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains A, C, D
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A, C, D
- GOL · Glycerol · additive · 2 copies · chains A, 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.83 | 0.84 | 118 | SGN, UAP, TLA, GOL |
| 2 | 55 | 0.32 | 0.77 | 15 | empty |
| 3 | 56 | 0.27 | 0.73 | 15 | empty |
| 4 | 50 | 0.24 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 781 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 533 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 336 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 103 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 76 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3OGX · 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 3OGX · PDBe 3OGX · UniProt Q9GK12
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