MolNFT v1 · #92662 · protein
Structural insights into the dual strategy of recognition of peptidoglycan recognition protein, pgrp-S: ternary complex of pgrp-S with lps and fatty acid
4GF9 · Peptidoglycan recognition protein 1: “Structural insights into the dual strategy of recognition of peptidoglycan recognition protein, pgrp-S…”. X-ray diffraction, 2 ligands (STE, LP5), 6 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 4GF9
- 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
- STE, LP5
- Pockets
- 6 · 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
- STE · Stearic acid · ligand · chains A, B, D
- LP5 · (R)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanamido)-6-(phosphonooxy) tetrahydro-2H-pyran-4-yl) 3-hydroxytetradecanoate · ligand · chains A, C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 774 | 0.83 | 0.86 | 91 | LP5, GOL |
| 2 | 120 | 0.67 | 0.89 | 31 | empty |
| 3 | 191 | 0.54 | 0.79 | 29 | STE |
| 4 | 92 | 0.38 | 0.76 | 19 | empty |
| 5 | 81 | 0.33 | 0.75 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 698 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 360 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4GF9 · Structural insights into the dual strategy of recognition of peptidoglycan recognition… · 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 0.96
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 4GF9 · PDBe 4GF9 · UniProt Q9GK12
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