Research workbench
Crystal structure of human pgrp-ibetac in complex with glycosamyl muramyl pentapeptide
Analyse Crystal structure of human pgrp-ibetac in complex with glycosamyl muramyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EAX
- Type
- protein
- Length
- 497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan recognition protein-I-beta; Glycosamyl muramyl pentapeptide
- UniProt
- Q3B822
- Ligands
- AMV, NAG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Peptidoglycan recognition protein-I-beta | protein | 164 | 32% helix, 21% strand | Q3B822 |
| L | Glycosamyl muramyl pentapeptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- AMV · methyl 2-acetamido-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside · ligand · chains C, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.65 | 0.77 | 56 | empty |
| 2 | 81 | 0.42 | 0.80 | 16 | empty |
| 3 | 98 | 0.40 | 0.77 | 21 | empty |
| 4 | 101 | 0.35 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 440 Ų buried · 1 hydrogen bond · protein-protein
- C–L · 354 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 310 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 119 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 d-amino, 1 covalent, 1 modified (disulfide, D-amino acid, covalent ligand, nonstandard).
Compared structures
- 2EAX · Crystal structure of human PGRP-IBETAC in complex with glycosamyl muramyl pentapeptide · the same entry in another collection · chain A against A, TM-score 1.00
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 Q3B822
- Elsewhere: RCSB PDB 2EAX · PDBe 2EAX · UniProt Q3B822
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.