Research workbench
Crystal structure of the ternary complex of peptidoglycan recognition protein, pgrp-S with hexanoic and tartaric acids at 2.07 a resolution.
Analyse Crystal structure of the ternary complex of peptidoglycan recognition protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XFW
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein 1
- UniProt
- Q9GK12
- Ligands
- 6NA, CL
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 166 | 29% helix, 20% strand | Q9GK12 |
Ligands and binding sites
- 6NA · Hexanoic acid · ligand · chains C, D
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, C
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, C, D
- ACT · Acetate ion · additive · 3 copies · chains B, C
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.80 | 0.82 | 103 | EDO, TLA, 6NA, GOL |
| 2 | 82 | 0.32 | 0.73 | 14 | empty |
| 3 | 58 | 0.31 | 0.76 | 20 | empty |
| 4 | 64 | 0.29 | 0.73 | 11 | empty |
| 5 | 50 | 0.26 | 0.74 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 655 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 549 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7XFW · Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S… · 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 0.99
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 7XFW · PDBe 7XFW · UniProt Q9GK12
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