Research workbench
Structure of the ternary complex of peptidoglycan recognition protein- short (pgrp-S) with hexanoic acid and tartaric acid at 2.30A resolution
Analyse Structure of the ternary complex of peptidoglycan recognition protein- short… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DY5
- 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
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 166 | 31% 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 · 4 copies · chains A, D, C
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 2 copies · chains A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.80 | 0.82 | 108 | EDO, 6NA, TLA, GOL |
| 2 | 60 | 0.69 | 0.96 | 24 | empty |
| 3 | 139 | 0.39 | 0.73 | 22 | empty |
| 4 | 51 | 0.25 | 0.73 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 652 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 531 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 15 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 7DY5 · Structure of the ternary complex of peptidoglycan recognition protein-short (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 0.99
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 7DY5 · PDBe 7DY5 · UniProt Q9GK12
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