MolNFT v1 · #140072 · protein
The X-tay structure of bumblebee pgrp-sa
5XZ4 · Bumblebee peptidoglycan recognition protein sa: “The X-tay structure of bumblebee pgrp-sa”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.81). MolNFT v1 #140072 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XZ4
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bumblebee peptidoglycan recognition protein sa
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bumblebee peptidoglycan recognition protein sa | protein | 167 | 29% helix, 20% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 848 | 0.81 | 0.84 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 630 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5XZ4 · The X-tay structure of Bumblebee 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
- Elsewhere: RCSB PDB 5XZ4 · PDBe 5XZ4
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