Research workbench
Crystal structure of human pgrp-ialphac in complex with muramyl pentapeptide
Analyse Crystal structure of human pgrp-ialphac in complex with muramyl pentapeptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2APH
- Type
- protein
- Length
- 340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein I-alpha; Muramyl pentapeptide
- UniProt
- Q96LB9
- Ligands
- AMU, NH2, SO4
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptidoglycan recognition protein I-alpha | protein | 165 | 27% helix, 20% strand | Q96LB9 |
| C, D | Muramyl pentapeptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- AMU · N-acetyl-beta-muramic acid · ligand · 2 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.77 | 34 | empty |
Interfaces
4 interfaces between chains.
- B–D · 426 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 143 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 110 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 d-amino, 2 covalent, 2 modified (disulfide, D-amino acid, covalent ligand, nonstandard).
Compared structures
- 2APH · Crystal structure of human PGRP-IalphaC in complex with muramyl pentapeptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q96LB9 · AlphaFold monomer V2.0 prediction for peptidoglycan recognition protein 3 (Q96LB9) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q96LB9
- Elsewhere: RCSB PDB 2APH · PDBe 2APH · UniProt Q96LB9
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