MolNFT v1 · #139478 · protein
Crystal structure of peptidoglycan recognition protein (pgrp-S) at 2.45 a resolution
5XGY · Peptidoglycan recognition protein 1: “Crystal structure of peptidoglycan recognition protein (pgrp-S) at 2.45 a resolution”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #139478 on GenesisL1: 3D structure…
- PDB
- 5XGY
- 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
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 33% helix, 20% strand | Q9GK12 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.82 | 0.86 | 89 | GOL, TLA |
| 2 | 180 | 0.54 | 0.79 | 37 | empty |
| 3 | 82 | 0.43 | 0.80 | 19 | empty |
| 4 | 65 | 0.36 | 0.77 | 15 | empty |
| 5 | 55 | 0.27 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 693 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 510 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 80 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 64 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5XGY · Crystal structure of peptidoglycan recognition protein (PGRP-S) at 2.45 A resolution · 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 0.99
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 5XGY · PDBe 5XGY · UniProt Q9GK12
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