Research workbench
Ternary complex of peptidoglycan recognition protein (pgrp-S) with maltose and N-acetylglucosamine at 1.7 a resolution
Analyse Ternary complex of peptidoglycan recognition protein (pgrp-S) with maltose and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NG4
- 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
- SRT, GLC, NAG
- Pockets
- 2 · 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
- SRT · S,R meso-tartaric acid · ligand · chains C, D
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C, D
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.83 | 0.84 | 129 | GLC, SRT, NAG, GOL |
| 2 | 103 | 0.47 | 0.80 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 823 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 523 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 155 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 80 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 3NG4 · Ternary complex of peptidoglycan recognition protein (PGRP-S) with Maltose and… · 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 3NG4 · PDBe 3NG4 · UniProt Q9GK12
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