MolNFT v1 · #140071 · protein
The X-ray structure of apis mellifera pgrp-sa
5XZ3 · Peptidoglycan-recognition protein: “The X-ray structure of apis mellifera pgrp-sa”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.78). MolNFT v1 #140071 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5XZ3
- Type
- protein
- Length
- 671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidoglycan-recognition protein
- UniProt
- A0A088AJM6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidoglycan-recognition protein | protein | 173 | 30% helix, 20% strand | A0A088AJM6 |
| B | Peptidoglycan-recognition protein | protein | 168 | 30% helix, 20% strand | A0A088AJM6 |
| C, D | Peptidoglycan-recognition protein | protein | 165 | 28% helix, 20% strand | A0A088AJM6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.78 | 0.83 | 62 | empty |
| 2 | 845 | 0.77 | 0.80 | 79 | SO4 |
| 3 | 219 | 0.55 | 0.78 | 26 | empty |
| 4 | 50 | 0.25 | 0.73 | 14 | empty |
| 5 | 50 | 0.24 | 0.73 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 670 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 641 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 203 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 198 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5XZ3 · The X-ray structure of Apis mellifera PGRP-SA · 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 A0A088AJM6
- Elsewhere: RCSB PDB 5XZ3 · PDBe 5XZ3 · UniProt A0A088AJM6
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