MolNFT v1 · #81306 · protein
Crystal structure of peptidoglycan recognition protein-S complexed with butyric acid at 2.2 a resolution
3UMQ · Peptidoglycan recognition protein 1: “Crystal structure of peptidoglycan recognition protein-S complexed with butyric acid at 2.2 a resolution”. X-ray diffraction, 1 ligand (BUA), 3 pockets (best druggability 0.84). MolNFT v1 #81306…
- PDB
- 3UMQ
- 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
- Ligands
- BUA
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Peptidoglycan recognition protein 1 | protein | 171 | 26% helix, 19% strand | Q9GK12 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 979 | 0.84 | 0.85 | 116 | GOL |
| 2 | 101 | 0.64 | 0.89 | 28 | BUA |
| 3 | 124 | 0.35 | 0.72 | 28 | empty |
Interfaces
5 interfaces between chains.
- A–B · 782 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 531 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 341 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 138 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3UMQ · Crystal structure of peptidoglycan recognition protein-S complexed with butyric acid at… · 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 0.97
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 3UMQ · PDBe 3UMQ · UniProt Q9GK12
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